chr7-62629538-A-G

Variant names:

• chr7-62629538-A-G
• rs2198427

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.704 in 150,616 control chromosomes in the GnomAD database, including 37,445 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 0.70 (37445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.704 AC: 105905 AN: 150498 Hom.: 37401 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.704 AC: 105996 AN: 150616 Hom.: 37445 Cov.: 32 AF XY: 0.713 AC XY: 52430 AN XY: 73558

African (AFR) AF: 0.697 AC: 28786 AN: 41300

American (AMR) AF: 0.796 AC: 11962 AN: 15030

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2198 AN: 3434

East Asian (EAS) AF: 0.823 AC: 4193 AN: 5092

South Asian (SAS) AF: 0.750 AC: 3607 AN: 4810

European-Finnish (FIN) AF: 0.776 AC: 8194 AN: 10562

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 44742 AN: 67100

Other (OTH) AF: 0.719 AC: 1498 AN: 2084

Alfa AF: 0.670 Hom.: 4180

Bravo AF: 0.709

Asia WGS AF: 0.763 AC: 2654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.5
DANN	Benign	0.28

Splicing

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

Other links and lift over

dbSNP: rs2198427; hg19: chr7-62089916;