5-63955835-T-C

Variant names:

• chr5-63955835-T-C
• rs1423691

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 0.586 in 152,062 control chromosomes in the GnomAD database, including 27,417 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 (27417 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.541
• Publications: 27 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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: 0.586 AC: 89028 AN: 151944 Hom.: 27376 Cov.: 32

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.586 AC: 89116 AN: 152062 Hom.: 27417 Cov.: 32 AF XY: 0.583 AC XY: 43360 AN XY: 74312

African (AFR) AF: 0.765 AC: 31718 AN: 41486

American (AMR) AF: 0.525 AC: 8010 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1857 AN: 3470

East Asian (EAS) AF: 0.792 AC: 4082 AN: 5156

South Asian (SAS) AF: 0.590 AC: 2842 AN: 4818

European-Finnish (FIN) AF: 0.425 AC: 4497 AN: 10574

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34060 AN: 67982

Other (OTH) AF: 0.579 AC: 1219 AN: 2106

Alfa AF: 0.525 Hom.: 11271

Bravo AF: 0.601

Asia WGS AF: 0.670 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	3.2
DANN	Benign	0.88
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1423691; hg19: chr5-63251662;