7-12125657-T-G

Variant names:

• chr7-12125657-T-G
• rs2356057

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 0.0358 in 151,470 control chromosomes in the GnomAD database, including 181 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 0.036 (181 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.380
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 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: 0.0358 AC: 5416 AN: 151364 Hom.: 181 Cov.: 32

Gnomad AFR AF: 0.0456

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0361

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.0135

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0196

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0358 AC: 5421 AN: 151470 Hom.: 181 Cov.: 32 AF XY: 0.0381 AC XY: 2816 AN XY: 73990

African (AFR) AF: 0.0455 AC: 1879 AN: 41284

American (AMR) AF: 0.0302 AC: 459 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.0361 AC: 125 AN: 3460

East Asian (EAS) AF: 0.142 AC: 733 AN: 5150

South Asian (SAS) AF: 0.128 AC: 615 AN: 4806

European-Finnish (FIN) AF: 0.0135 AC: 140 AN: 10368

Middle Eastern (MID) AF: 0.0651 AC: 19 AN: 292

European-Non Finnish (NFE) AF: 0.0196 AC: 1330 AN: 67892

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0137 Hom.: 14

Bravo AF: 0.0373

Asia WGS AF: 0.136 AC: 472 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.9
DANN	Benign	0.61
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs2356057; hg19: chr7-12165283; COSMIC: COSV66718128;