rs13082711

chr3-27496418-T-C

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 0.165 in 152,048 control chromosomes in the GnomAD database, including 2,418 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 0.16 (2418 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25013 AN: 151930 Hom.: 2419 Cov.: 31

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.165 AC: 25020 AN: 152048 Hom.: 2418 Cov.: 31 AF XY: 0.161 AC XY: 11962 AN XY: 74308

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.0463

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.153

Alfa AF: 0.214 Hom.: 3817

Bravo AF: 0.159

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.0
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13082711; hg19: chr3-27537909;