13-61246864-C-T

Variant names:

• chr13-61246864-C-T
• rs2170765

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 0.545 in 152,036 control chromosomes in the GnomAD database, including 23,831 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 0.55 (23831 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 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: 0.545 AC: 82802 AN: 151918 Hom.: 23800 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.545 AC: 82883 AN: 152036 Hom.: 23831 Cov.: 32 AF XY: 0.540 AC XY: 40155 AN XY: 74298

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.264

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.496

Gnomad4 OTH AF: 0.525

Alfa AF: 0.503 Hom.: 8910

Bravo AF: 0.551

Asia WGS AF: 0.369 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2170765; hg19: chr13-61820997;