rs10517855

chr4-63254441-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.0564

Gnomad4 ASJ AF: 0.0326

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0211

Gnomad4 NFE AF: 0.0293

Gnomad4 OTH AF: 0.0332

Alfa AF: 0.0361 Hom.: 17

Bravo AF: 0.0402

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.9
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517855; hg19: chr4-64120159;