Genetic Variant NM_019644.4:c.144G>A (chr7-118224974-G-A) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_019644.4(ANKRD7):c.144G>A(p.Lys48Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 1,614,048 control chromosomes in the GnomAD database, including 509 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.018 ( 44 hom., cov: 31)

Exomes 𝑓: 0.015 ( 465 hom. )

Consequence

ANKRD7
NM_019644.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.38

Publications

9 publications found

Variant links:

Genes affected

ANKRD7 (HGNC:18588): (ankyrin repeat domain 7) Predicted to act upstream of or within blastocyst hatching. Located in centrosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ANKRD7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP7

Synonymous conserved (PhyloP=1.38 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019644.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD7	NM_019644.4	MANE Select	c.144G>A	p.Lys48Lys	synonymous	Exon 1 of 7	NP_062618.2	Q92527-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
ANKRD7	ENST00000265224.9	TSL:1 MANE Select	c.144G>A	p.Lys48Lys	synonymous	Exon 1 of 7	ENSP00000265224.4	Q92527-1
ANKRD7	ENST00000417525.5	TSL:5	c.144G>A	p.Lys48Lys	synonymous	Exon 1 of 7	ENSP00000395595.2	C9JIJ7
ANKRD7	ENST00000486422.1	TSL:3	c.144G>A	p.Lys48Lys	synonymous	Exon 1 of 3	ENSP00000417353.1	C9J2M7

Frequencies

GnomAD3 genomes

AF:

0.0184

AC:

2793

AN:

152156

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0188

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0415

Gnomad ASJ

AF:

0.0199

Gnomad EAS

AF:

0.0773

Gnomad SAS

AF:

0.0286

Gnomad FIN

AF:

0.00951

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.00913

Gnomad OTH

AF:

0.0182

GnomAD2 exomes

AF:

0.0293

AC:

7239

AN:

247188

AF XY:

0.0255

show subpopulations

Gnomad AFR exome

AF:

0.0191

Gnomad AMR exome

AF:

0.0931

Gnomad ASJ exome

AF:

0.0228

Gnomad EAS exome

AF:

0.0815

Gnomad FIN exome

AF:

0.00728

Gnomad NFE exome

AF:

0.00877

Gnomad OTH exome

AF:

0.0240

GnomAD4 exome

AF:

0.0149

AC:

21708

AN:

1461774

Hom.:

465

Cov.:

AF XY:

0.0148

AC XY:

10736

AN XY:

727194

show subpopulations

African (AFR)

AF:

0.0198

AC:

662

AN:

33470

American (AMR)

AF:

0.0828

AC:

3702

AN:

44690

Ashkenazi Jewish (ASJ)

AF:

0.0214

AC:

560

AN:

26128

East Asian (EAS)

AF:

0.0775

AC:

3076

AN:

39696

South Asian (SAS)

AF:

0.0250

AC:

2156

AN:

86250

European-Finnish (FIN)

AF:

0.00638

AC:

341

AN:

53412

Middle Eastern (MID)

AF:

0.0333

AC:

192

AN:

5768

European-Non Finnish (NFE)

AF:

0.00904

AC:

10049

AN:

1111970

Other (OTH)

AF:

0.0161

AC:

970

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

1093

2185

3278

4370

5463

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

502

1004

1506

2008

2510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0183

AC:

2793

AN:

152274

Hom.:

Cov.:

AF XY:

0.0198

AC XY:

1472

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.0187

AC:

777

AN:

41556

American (AMR)

AF:

0.0416

AC:

637

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0199

AC:

AN:

3468

East Asian (EAS)

AF:

0.0771

AC:

399

AN:

5174

South Asian (SAS)

AF:

0.0288

AC:

139

AN:

4822

European-Finnish (FIN)

AF:

0.00951

AC:

101

AN:

10622

Middle Eastern (MID)

AF:

0.0408

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00910

AC:

619

AN:

68010

Other (OTH)

AF:

0.0189

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

130

261

391

522

652

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

160

200

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00622

Hom.:

Bravo

AF:

0.0227

EpiCase

AF:

0.0115

EpiControl

AF:

0.0106

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.4

(source)

DANN

Benign

0.43

PhyloP100

1.4

PromoterAI

-0.069

Neutral

(source)

Mutation Taster

=300/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over