rs7955516

Variant names:

• chr12-20345102-A-C
• rs7955516

Your query was ambiguous. Multiple possible variants found:

• chr12-20345102-A-C
• chr12-20345102-A-G
• chr12-20345102-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 0.357 in 145,616 control chromosomes in the GnomAD database, including 9,261 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 0.36 (9261 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.36
• Publications: 25 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 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: 0.357 AC: 51988 AN: 145494 Hom.: 9253 Cov.: 29

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.451

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.357 AC: 52024 AN: 145616 Hom.: 9261 Cov.: 29 AF XY: 0.352 AC XY: 25055 AN XY: 71198

African (AFR) AF: 0.311 AC: 12165 AN: 39090

American (AMR) AF: 0.420 AC: 6213 AN: 14808

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1349 AN: 3324

East Asian (EAS) AF: 0.119 AC: 559 AN: 4682

South Asian (SAS) AF: 0.322 AC: 1440 AN: 4466

European-Finnish (FIN) AF: 0.303 AC: 3130 AN: 10340

Middle Eastern (MID) AF: 0.451 AC: 128 AN: 284

European-Non Finnish (NFE) AF: 0.393 AC: 25841 AN: 65708

Other (OTH) AF: 0.383 AC: 774 AN: 2020

Alfa AF: 0.364 Hom.: 28503

Bravo AF: 0.351

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.016
DANN	Benign	0.21
PhyloP100		-4.4

Splicing

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

Other links and lift over

dbSNP: rs7955516; hg19: chr12-20498036;