rs10517863

Variant names:

• chr4-63661682-G-T
• rs10517863

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 0.0448 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0782 AC: 3243 AN: 41466

American (AMR) AF: 0.0223 AC: 339 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3472

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5154

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4824

European-Finnish (FIN) AF: 0.0361 AC: 382 AN: 10596

Middle Eastern (MID) AF: 0.0621 AC: 18 AN: 290

European-Non Finnish (NFE) AF: 0.0335 AC: 2266 AN: 67608

Other (OTH) AF: 0.0352 AC: 74 AN: 2104

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
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10517863; hg19: chr4-64527400;