Genetic Variant ENSG00000226471:n.176G>C (chr22-28800855-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000585003.2(ENSG00000226471):n.176G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 361,402 control chromosomes in the GnomAD database, including 3,580 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 0.10 ( 1099 hom., cov: 33)

Exomes 𝑓: 0.14 ( 2481 hom. )

Consequence

ENSG00000226471
ENST00000585003.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

5 publications found

Variant links:

Genes affected

ENSG00000226471 (HGNC:):

ENSG00000226471 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000226471	ENST00000585003.2 link	n.176G>C	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000226471	ENST00000418292.1 link	n.34+118G>C	intron_variant	Intron 1 of 1	3
ENSG00000226471	ENST00000458080.2 link	n.55+118G>C	intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes

AF:

0.103

AC:

15692

AN:

152158

Hom.:

1101

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0246

Gnomad AMI

AF:

0.0912

Gnomad AMR

AF:

0.0817

Gnomad ASJ

AF:

0.130

Gnomad EAS

AF:

0.206

Gnomad SAS

AF:

0.281

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.203

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.131

GnomAD4 exome

AF:

0.143

AC:

29825

AN:

209126

Hom.:

2481

Cov.:

AF XY:

0.148

AC XY:

15939

AN XY:

107368

show subpopulations

African (AFR)

AF:

0.0256

AC:

129

AN:

5040

American (AMR)

AF:

0.0773

AC:

365

AN:

4720

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

881

AN:

7156

East Asian (EAS)

AF:

0.200

AC:

3105

AN:

15552

South Asian (SAS)

AF:

0.284

AC:

3555

AN:

12508

European-Finnish (FIN)

AF:

0.110

AC:

1922

AN:

17538

Middle Eastern (MID)

AF:

0.232

AC:

239

AN:

1028

European-Non Finnish (NFE)

AF:

0.135

AC:

17824

AN:

132060

Other (OTH)

AF:

0.133

AC:

1805

AN:

13524

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

1139

2279

3418

4558

5697

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

172

258

344

430

<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:

0.103

AC:

15684

AN:

152276

Hom.:

1099

Cov.:

AF XY:

0.104

AC XY:

7763

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.0245

AC:

1018

AN:

41566

American (AMR)

AF:

0.0816

AC:

1248

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.130

AC:

452

AN:

3470

East Asian (EAS)

AF:

0.206

AC:

1065

AN:

5178

South Asian (SAS)

AF:

0.280

AC:

1352

AN:

4822

European-Finnish (FIN)

AF:

0.101

AC:

1068

AN:

10612

Middle Eastern (MID)

AF:

0.211

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9061

AN:

68022

Other (OTH)

AF:

0.130

AC:

275

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

739

1478

2217

2956

3695

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

196

392

588

784

980

<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:

0.0575

Hom.:

Bravo

AF:

0.0961

Asia WGS

AF:

0.239

AC:

832

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

8.6

(source)

DANN

Benign

0.75

PhyloP100

-1.1

PromoterAI

0.048

Neutral

(source)

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over