13-61617230-C-T

Variant names:

• chr13-61617230-C-T
• rs2329302

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 0.575 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
• Publications: 0 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.850 AC: 35178 AN: 41402

American (AMR) AF: 0.489 AC: 7407 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1802 AN: 3462

East Asian (EAS) AF: 0.297 AC: 1529 AN: 5152

South Asian (SAS) AF: 0.396 AC: 1903 AN: 4802

European-Finnish (FIN) AF: 0.477 AC: 5026 AN: 10540

Middle Eastern (MID) AF: 0.493 AC: 142 AN: 288

European-Non Finnish (NFE) AF: 0.481 AC: 32529 AN: 67698

Other (OTH) AF: 0.547 AC: 1148 AN: 2098

Alfa AF: 0.562 Hom.: 3315

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2329302; hg19: chr13-62191363;