13-61617230-C-T

Position:

• chr13-61617230-C-T

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 0.575 in 151,502 control chromosomes in the GnomAD database, including 27,224 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 0.57 (27224 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.842 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: 0.575 AC: 87020 AN: 151384 Hom.: 27180 Cov.: 31

Gnomad AFR AF: 0.849

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.575 AC: 87111 AN: 151502 Hom.: 27224 Cov.: 31 AF XY: 0.570 AC XY: 42145 AN XY: 73998

Gnomad4 AFR AF: 0.850

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.547

Alfa AF: 0.551 Hom.: 3036

Bravo AF: 0.585

Asia WGS AF: 0.391 AC: 1363 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.50
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2329302; hg19: chr13-62191363;