7-128735983-A-G

Variant names:

• chr7-128735983-A-G
• rs2402934

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 0.114 in 152,146 control chromosomes in the GnomAD database, including 1,976 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 (1976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17288 AN: 152026 Hom.: 1974 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.114 AC: 17300 AN: 152146 Hom.: 1976 Cov.: 32 AF XY: 0.121 AC XY: 8978 AN XY: 74380

African (AFR) AF: 0.0651 AC: 2702 AN: 41516

American (AMR) AF: 0.251 AC: 3842 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3466

East Asian (EAS) AF: 0.584 AC: 3012 AN: 5158

South Asian (SAS) AF: 0.187 AC: 899 AN: 4820

European-Finnish (FIN) AF: 0.108 AC: 1139 AN: 10592

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0765 AC: 5203 AN: 68000

Other (OTH) AF: 0.104 AC: 220 AN: 2112

Alfa AF: 0.114 Hom.: 677

Bravo AF: 0.127

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.54
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2402934; hg19: chr7-128376037;