13-42701010-T-C

Variant names:

• chr13-42701010-T-C
• rs6561072

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 0.514 in 152,106 control chromosomes in the GnomAD database, including 21,337 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 0.51 (21337 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

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 (AFR) allele frequency at 95% confidence interval = 0.693 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: 0.514 AC: 78070 AN: 151988 Hom.: 21304 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.514 AC: 78148 AN: 152106 Hom.: 21337 Cov.: 33 AF XY: 0.516 AC XY: 38385 AN XY: 74350

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.374

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.493

Alfa AF: 0.416 Hom.: 6654

Bravo AF: 0.530

Asia WGS AF: 0.410 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6561072; hg19: chr13-43275146; COSMIC: COSV69348122;