dbSNP rs10499320: ENSG00000217455:n.76-6360C>G (chr7-3093749-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 ENST00000667422.1(ENSG00000217455):n.76-6360C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,032 control chromosomes in the GnomAD database, including 1,090 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 ( 1090 hom., cov: 31)

Consequence

ENSG00000217455
ENST00000667422.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.148

Publications

2 publications found

Variant links:

Genes affected

ENSG00000217455 (HGNC:):

ENSG00000217455 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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
ENSG00000217455	ENST00000667422.1 link	n.76-6360C>G	intron_variant	Intron 1 of 1
ENSG00000217455	ENST00000716171.1 link	n.249-7329C>G	intron_variant	Intron 3 of 4
ENSG00000217455	ENST00000810303.1 link	n.186-7329C>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

17272

AN:

151914

Hom.:

1088

Cov.:

show subpopulations

Gnomad AFR

AF:

0.100

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.0898

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.0302

Gnomad SAS

AF:

0.163

Gnomad FIN

AF:

0.0629

Gnomad MID

AF:

0.104

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.114

AC:

17269

AN:

152032

Hom.:

1090

Cov.:

AF XY:

0.112

AC XY:

8319

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.0999

AC:

4138

AN:

41440

American (AMR)

AF:

0.0896

AC:

1368

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

687

AN:

3470

East Asian (EAS)

AF:

0.0303

AC:

157

AN:

5182

South Asian (SAS)

AF:

0.163

AC:

781

AN:

4804

European-Finnish (FIN)

AF:

0.0629

AC:

665

AN:

10566

Middle Eastern (MID)

AF:

0.112

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.133

AC:

9065

AN:

67986

Other (OTH)

AF:

0.130

AC:

275

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

767

1535

2302

3070

3837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.120

Hom.:

149

Bravo

AF:

0.112

Asia WGS

AF:

0.0720

AC:

251

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.2

(source)

DANN

Benign

0.44

PhyloP100

-0.15

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