rs10517863

Variant names:

• chr4-63661682-G-T
• rs10517863

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 0.0448 in 151,606 control chromosomes in the GnomAD database, including 188 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 0.045 (188 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.076 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: 0.0448 AC: 6783 AN: 151488 Hom.: 188 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0224

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.0361

Gnomad MID AF: 0.0613

Gnomad NFE AF: 0.0335

Gnomad OTH AF: 0.0355

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

GnomAD4 genome AF: 0.0448 AC: 6793 AN: 151606 Hom.: 188 Cov.: 32 AF XY: 0.0444 AC XY: 3285 AN XY: 74068

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0223

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.0361

Gnomad4 NFE AF: 0.0335

Gnomad4 OTH AF: 0.0352

Alfa AF: 0.0402 Hom.: 14

Bravo AF: 0.0446

Asia WGS AF: 0.0190 AC: 68 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517863; hg19: chr4-64527400;