13-65326561-T-C

Variant names:

• chr13-65326561-T-C
• rs965281

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 0.177 in 152,138 control chromosomes in the GnomAD database, including 2,714 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 0.18 (2714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.595
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.447 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: 0.177 AC: 26953 AN: 152018 Hom.: 2703 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.177 AC: 26980 AN: 152138 Hom.: 2714 Cov.: 31 AF XY: 0.182 AC XY: 13555 AN XY: 74380

African (AFR) AF: 0.122 AC: 5086 AN: 41524

American (AMR) AF: 0.230 AC: 3517 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2383 AN: 5152

South Asian (SAS) AF: 0.285 AC: 1373 AN: 4824

European-Finnish (FIN) AF: 0.170 AC: 1804 AN: 10592

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11039 AN: 67976

Other (OTH) AF: 0.225 AC: 475 AN: 2112

Alfa AF: 0.174 Hom.: 2862

Bravo AF: 0.179

Asia WGS AF: 0.368 AC: 1278 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	0.78
DANN	Benign	0.70
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs965281; hg19: chr13-65900693;