7-38088724-T-C

Variant names:

• chr7-38088724-T-C
• rs6959212

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 0.648 in 151,944 control chromosomes in the GnomAD database, including 32,116 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 0.65 (32116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 70 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.658 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: 0.648 AC: 98335 AN: 151826 Hom.: 32074 Cov.: 32

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.648 AC: 98443 AN: 151944 Hom.: 32116 Cov.: 32 AF XY: 0.649 AC XY: 48229 AN XY: 74280

African (AFR) AF: 0.647 AC: 26784 AN: 41428

American (AMR) AF: 0.535 AC: 8155 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2345 AN: 3472

East Asian (EAS) AF: 0.677 AC: 3496 AN: 5164

South Asian (SAS) AF: 0.630 AC: 3035 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7918 AN: 10570

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.656 AC: 44534 AN: 67920

Other (OTH) AF: 0.652 AC: 1378 AN: 2112

Alfa AF: 0.643 Hom.: 31909

Bravo AF: 0.635

Asia WGS AF: 0.651 AC: 2257 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.40
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6959212; hg19: chr7-38128326; COSMIC: COSV66544360;