dbSNP rs6741418: ENSG00000228509:n.201+9012G>A (chr2-190858993-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000772372.1(ENSG00000228509):n.201+9012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,142 control chromosomes in the GnomAD database, including 1,162 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 0.11 ( 1162 hom., cov: 32)

Consequence

ENSG00000228509
ENST00000772372.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.03

Publications

5 publications found

Variant links:

Genes affected

ENSG00000228509 (HGNC:):

ENSG00000228509 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228509	ENST00000772372.1 link	n.201+9012G>A		intron_variant	Intron 3 of 4
ENSG00000228509	ENST00000772376.1 link	n.302+2873G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16274

AN:

152024

Hom.:

1161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0293

Gnomad AMI

AF:

0.259

Gnomad AMR

AF:

0.115

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.000963

Gnomad SAS

AF:

0.0467

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.158

Gnomad NFE

AF:

0.157

Gnomad OTH

AF:

0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.107

AC:

16277

AN:

152142

Hom.:

1162

Cov.:

AF XY:

0.105

AC XY:

7772

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.0293

AC:

1216

AN:

41538

American (AMR)

AF:

0.114

AC:

1749

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.186

AC:

645

AN:

3470

East Asian (EAS)

AF:

0.000965

AC:

AN:

5182

South Asian (SAS)

AF:

0.0461

AC:

222

AN:

4818

European-Finnish (FIN)

AF:

0.115

AC:

1218

AN:

10566

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.157

AC:

10664

AN:

67974

Other (OTH)

AF:

0.129

AC:

272

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

709

1419

2128

2838

3547

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

174

348

522

696

870

<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:

0.149

Hom.:

2197

Bravo

AF:

0.107

Asia WGS

AF:

0.0240

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

(source)

DANN

Benign

0.75

PhyloP100

3.0

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over