rs1981186

Positions:

• chr13-72548063-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 0.61 in 151,604 control chromosomes in the GnomAD database, including 28,471 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 0.61 (28471 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 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: 0.610 AC: 92406 AN: 151498 Hom.: 28446 Cov.: 30

Gnomad AFR AF: 0.630

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.610 AC: 92488 AN: 151604 Hom.: 28471 Cov.: 30 AF XY: 0.604 AC XY: 44720 AN XY: 74048

Gnomad4 AFR AF: 0.630

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.591

Alfa AF: 0.615 Hom.: 28500

Bravo AF: 0.607

Asia WGS AF: 0.480 AC: 1660 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981186; hg19: chr13-73122201;