4-63254441-T-C

Variant names:

• chr4-63254441-T-C
• rs10517855

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 0.0397 in 152,172 control chromosomes in the GnomAD database, including 203 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 0.040 (203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0397 AC: 6035 AN: 152052 Hom.: 202 Cov.: 32

Gnomad AFR AF: 0.0291

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0211

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0292

Gnomad OTH AF: 0.0336

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

GnomAD4 genome AF: 0.0397 AC: 6042 AN: 152172 Hom.: 203 Cov.: 32 AF XY: 0.0427 AC XY: 3174 AN XY: 74414

African (AFR) AF: 0.0291 AC: 1209 AN: 41542

American (AMR) AF: 0.0564 AC: 863 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3470

East Asian (EAS) AF: 0.189 AC: 975 AN: 5158

South Asian (SAS) AF: 0.119 AC: 574 AN: 4820

European-Finnish (FIN) AF: 0.0211 AC: 224 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0293 AC: 1988 AN: 67954

Other (OTH) AF: 0.0332 AC: 70 AN: 2106

Alfa AF: 0.0341 Hom.: 30

Bravo AF: 0.0402

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.33
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10517855; hg19: chr4-64120159;