rs7780976

Variant names:

• chr7-14098974-A-C
• rs7780976

Your query was ambiguous. Multiple possible variants found:

• chr7-14098974-A-C
• chr7-14098974-A-T

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 0.274 in 151,746 control chromosomes in the GnomAD database, including 7,309 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 0.27 (7309 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 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: 0.274 AC: 41542 AN: 151628 Hom.: 7286 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.274 AC: 41590 AN: 151746 Hom.: 7309 Cov.: 32 AF XY: 0.275 AC XY: 20403 AN XY: 74172

African (AFR) AF: 0.498 AC: 20618 AN: 41392

American (AMR) AF: 0.206 AC: 3139 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3464

East Asian (EAS) AF: 0.319 AC: 1637 AN: 5134

South Asian (SAS) AF: 0.246 AC: 1186 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2200 AN: 10584

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11213 AN: 67808

Other (OTH) AF: 0.249 AC: 525 AN: 2108

Alfa AF: 0.210 Hom.: 9047

Bravo AF: 0.283

Asia WGS AF: 0.309 AC: 1073 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.2
DANN	Benign	0.31
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7780976; hg19: chr7-14138599; COSMIC: COSV56054045;