13-61246864-C-T

Variant names:

• chr13-61246864-C-T
• rs2170765

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 0.545 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.726 AC: 30132 AN: 41494

American (AMR) AF: 0.489 AC: 7473 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3470

East Asian (EAS) AF: 0.264 AC: 1359 AN: 5156

South Asian (SAS) AF: 0.445 AC: 2140 AN: 4808

European-Finnish (FIN) AF: 0.459 AC: 4846 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33709 AN: 67966

Other (OTH) AF: 0.525 AC: 1107 AN: 2108

Alfa AF: 0.502 Hom.: 9871

Bravo AF: 0.551

Asia WGS AF: 0.369 AC: 1288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.3
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2170765; hg19: chr13-61820997;