rs7971309

Variant names:

• chr12-108029499-C-T
• rs7971309

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 0.129 in 151,964 control chromosomes in the GnomAD database, including 3,175 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 0.13 (3175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 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: 0.129 AC: 19560 AN: 151844 Hom.: 3159 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.00374

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.00850

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00222

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.129 AC: 19621 AN: 151964 Hom.: 3175 Cov.: 32 AF XY: 0.130 AC XY: 9628 AN XY: 74268

African (AFR) AF: 0.359 AC: 14872 AN: 41388

American (AMR) AF: 0.143 AC: 2187 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.00374 AC: 13 AN: 3472

East Asian (EAS) AF: 0.284 AC: 1463 AN: 5160

South Asian (SAS) AF: 0.129 AC: 619 AN: 4816

European-Finnish (FIN) AF: 0.00850 AC: 90 AN: 10584

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00222 AC: 151 AN: 67984

Other (OTH) AF: 0.104 AC: 219 AN: 2100

Alfa AF: 0.0561 Hom.: 3190

Bravo AF: 0.151

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		-0.099

Splicing

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

Other links and lift over

dbSNP: rs7971309; hg19: chr12-108423276;