dbSNP rs1192514: ANKRD60:p.Arg119Arg (chr20-58228297-C-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001304369.2(ANKRD60):c.357G>A(p.Arg119Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 1,551,084 control chromosomes in the GnomAD database, including 62,922 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 0.28 ( 6218 hom., cov: 31)

Exomes 𝑓: 0.28 ( 56704 hom. )

Consequence

ANKRD60
NM_001304369.2 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

5 publications found

Variant links:

Genes affected

ANKRD60 (HGNC:16217): (ankyrin repeat domain 60)

ANKRD60 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -11 ACMG points.

BP4

Computational evidence support a benign effect (REVEL=0.024).

BP7

Synonymous conserved (PhyloP=0.159 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD60	NM_001304369.2 link	c.357G>A	p.Arg119Arg	synonymous_variant	Exon 1 of 4	ENST00000457363.2	NP_001291298.1	Q9BZ19
ANKRD60	XM_047439902.1 link	c.357G>A	p.Arg119Arg	synonymous_variant	Exon 1 of 4		XP_047295858.1
ANKRD60	XM_047439903.1 link	c.357G>A	p.Arg119Arg	synonymous_variant	Exon 1 of 4		XP_047295859.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ANKRD60	ENST00000457363.2 link	c.357G>A	p.Arg119Arg	synonymous_variant	Exon 1 of 4	5	NM_001304369.2	ENSP00000396747.1		Q9BZ19

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42341

AN:

151862

Hom.:

6201

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.132

Gnomad AMR

AF:

0.357

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.321

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.294

GnomAD2 exomes

AF:

0.327

AC:

50599

AN:

154606

AF XY:

0.331

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.449

Gnomad ASJ exome

AF:

0.398

Gnomad EAS exome

AF:

0.376

Gnomad FIN exome

AF:

0.201

Gnomad NFE exome

AF:

0.265

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.279

AC:

389942

AN:

1399104

Hom.:

56704

Cov.:

AF XY:

0.284

AC XY:

195717

AN XY:

690068

show subpopulations

African (AFR)

AF:

0.260

AC:

8204

AN:

31598

American (AMR)

AF:

0.437

AC:

15576

AN:

35682

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

9844

AN:

25180

East Asian (EAS)

AF:

0.304

AC:

10868

AN:

35738

South Asian (SAS)

AF:

0.421

AC:

33316

AN:

79224

European-Finnish (FIN)

AF:

0.204

AC:

10005

AN:

49120

Middle Eastern (MID)

AF:

0.318

AC:

1807

AN:

5688

European-Non Finnish (NFE)

AF:

0.262

AC:

283058

AN:

1078870

Other (OTH)

AF:

0.298

AC:

17264

AN:

58004

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

16188

32377

48565

64754

80942

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.279

AC:

42398

AN:

151980

Hom.:

6218

Cov.:

AF XY:

0.282

AC XY:

20935

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.261

AC:

10827

AN:

41466

American (AMR)

AF:

0.357

AC:

5460

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.389

AC:

1351

AN:

3472

East Asian (EAS)

AF:

0.371

AC:

1904

AN:

5134

South Asian (SAS)

AF:

0.416

AC:

2001

AN:

4810

European-Finnish (FIN)

AF:

0.207

AC:

2191

AN:

10588

Middle Eastern (MID)

AF:

0.321

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.262

AC:

17828

AN:

67924

Other (OTH)

AF:

0.296

AC:

623

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1510

3019

4529

6038

7548

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.281

Hom.:

4783

Bravo

AF:

0.288

Asia WGS

AF:

0.391

AC:

1357

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

8.8

(source)

DANN

Uncertain

0.98

PhyloP100

0.16

PromoterAI

0.0092

Neutral

(source)

Mutation Taster

=100/0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

rs1192514

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over