rs3812863

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;