5-63955271-T-C

Variant names:

• chr5-63955271-T-C
• rs970453

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 0.588 in 152,016 control chromosomes in the GnomAD database, including 27,647 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 0.59 (27647 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.772 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: 0.588 AC: 89321 AN: 151898 Hom.: 27601 Cov.: 31

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.588 AC: 89416 AN: 152016 Hom.: 27647 Cov.: 31 AF XY: 0.586 AC XY: 43504 AN XY: 74300

African (AFR) AF: 0.772 AC: 32001 AN: 41464

American (AMR) AF: 0.525 AC: 8023 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3468

East Asian (EAS) AF: 0.792 AC: 4087 AN: 5158

South Asian (SAS) AF: 0.591 AC: 2846 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4482 AN: 10542

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 34061 AN: 67980

Other (OTH) AF: 0.580 AC: 1226 AN: 2112

Alfa AF: 0.570 Hom.: 3703

Bravo AF: 0.603

Asia WGS AF: 0.671 AC: 2333 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.8
DANN	Benign	0.56
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs970453; hg19: chr5-63251098;