rs3812863

Variant names:

• chr13-27971131-G-A
• rs3812863

Your query was ambiguous. Multiple possible variants found:

• chr13-27971131-G-A
• chr13-27971131-G-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 0.479 in 152,040 control chromosomes in the GnomAD database, including 18,853 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 0.48 (18844 hom., cov: 32)
  • Exomes 𝑓: 0.74 (9 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.701 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: 0.480 AC: 72847 AN: 151882 Hom.: 18840 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.503

GnomAD4 exome AF: 0.737 AC: 28 AN: 38 Hom.: 9 Cov.: 0 AF XY: 0.773 AC XY: 17 AN XY: 22

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.765

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.479 AC: 72873 AN: 152002 Hom.: 18844 Cov.: 32 AF XY: 0.482 AC XY: 35804 AN XY: 74258

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.434

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.504

Alfa AF: 0.554 Hom.: 24399

Bravo AF: 0.447

Asia WGS AF: 0.577 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3812863; hg19: chr13-28545268;