7-12556990-T-C

Variant names:

• chr7-12556990-T-C
• rs11764174

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 0.611 in 151,932 control chromosomes in the GnomAD database, including 28,443 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 0.61 (28443 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.252
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 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: 0.611 AC: 92739 AN: 151814 Hom.: 28412 Cov.: 31

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.613

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.611 AC: 92814 AN: 151932 Hom.: 28443 Cov.: 31 AF XY: 0.606 AC XY: 44989 AN XY: 74242

African (AFR) AF: 0.633 AC: 26238 AN: 41430

American (AMR) AF: 0.642 AC: 9810 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2071 AN: 3464

East Asian (EAS) AF: 0.552 AC: 2840 AN: 5148

South Asian (SAS) AF: 0.472 AC: 2268 AN: 4806

European-Finnish (FIN) AF: 0.560 AC: 5895 AN: 10536

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.613 AC: 41685 AN: 67956

Other (OTH) AF: 0.596 AC: 1257 AN: 2110

Alfa AF: 0.613 Hom.: 70534

Bravo AF: 0.622

Asia WGS AF: 0.491 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.5
DANN	Benign	0.63
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs11764174; hg19: chr7-12596616;