rs7971309

Variant names:

• chr12-108029499-C-T
• rs7971309

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.00374

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.00850

Gnomad4 NFE AF: 0.00222

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0251 Hom.: 857

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7971309; hg19: chr12-108423276;