13-72548063-T-C

Variant names:

• chr13-72548063-T-C
• rs1981186

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.630 AC: 26028 AN: 41294

American (AMR) AF: 0.578 AC: 8803 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1962 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2049 AN: 5134

South Asian (SAS) AF: 0.560 AC: 2692 AN: 4806

European-Finnish (FIN) AF: 0.580 AC: 6046 AN: 10432

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.632 AC: 42948 AN: 67922

Other (OTH) AF: 0.591 AC: 1246 AN: 2110

Alfa AF: 0.615 Hom.: 37016

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1981186; hg19: chr13-73122201;