chr7-129186970-G-C

Variant names:

• chr7-129186970-G-C
• rs6962740

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 0.239 in 151,956 control chromosomes in the GnomAD database, including 4,530 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 0.24 (4530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36284 AN: 151838 Hom.: 4525 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.239 AC: 36322 AN: 151956 Hom.: 4530 Cov.: 32 AF XY: 0.241 AC XY: 17921 AN XY: 74286

African (AFR) AF: 0.270 AC: 11194 AN: 41414

American (AMR) AF: 0.268 AC: 4085 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 535 AN: 3472

East Asian (EAS) AF: 0.186 AC: 963 AN: 5172

South Asian (SAS) AF: 0.215 AC: 1038 AN: 4818

European-Finnish (FIN) AF: 0.283 AC: 2984 AN: 10562

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14913 AN: 67952

Other (OTH) AF: 0.221 AC: 466 AN: 2106

Alfa AF: 0.111 Hom.: 180

Bravo AF: 0.238

Asia WGS AF: 0.234 AC: 817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6962740; hg19: chr7-128826811;