13-64582995-C-T

Variant names:

• chr13-64582995-C-T
• rs7996275

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 0.452 in 151,404 control chromosomes in the GnomAD database, including 16,362 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 0.45 (16362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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: 0.452 AC: 68391 AN: 151284 Hom.: 16362 Cov.: 32

Gnomad AFR AF: 0.303

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.635

Gnomad NFE AF: 0.529

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.452 AC: 68390 AN: 151404 Hom.: 16362 Cov.: 32 AF XY: 0.452 AC XY: 33451 AN XY: 73942

African (AFR) AF: 0.302 AC: 12515 AN: 41394

American (AMR) AF: 0.417 AC: 6326 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1884 AN: 3462

East Asian (EAS) AF: 0.426 AC: 2193 AN: 5144

South Asian (SAS) AF: 0.482 AC: 2317 AN: 4806

European-Finnish (FIN) AF: 0.528 AC: 5530 AN: 10478

Middle Eastern (MID) AF: 0.641 AC: 168 AN: 262

European-Non Finnish (NFE) AF: 0.529 AC: 35832 AN: 67680

Other (OTH) AF: 0.502 AC: 1053 AN: 2098

Alfa AF: 0.395 Hom.: 5102

Bravo AF: 0.436

Asia WGS AF: 0.403 AC: 1381 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.53
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs7996275; hg19: chr13-65157127;