rs10517830

Variant names:

• chr4-62840506-T-C
• rs10517830

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 152,190 control chromosomes in the GnomAD database, including 226 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 (226 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.165
• Publications: 3 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 = 0.0776 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: 6817 AN: 152072 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.0801

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0791

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.0355

Gnomad SAS AF: 0.0408

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0146

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0448 AC: 6823 AN: 152190 Hom.: 226 Cov.: 32 AF XY: 0.0472 AC XY: 3513 AN XY: 74398

African (AFR) AF: 0.0799 AC: 3317 AN: 41526

American (AMR) AF: 0.0793 AC: 1210 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3472

East Asian (EAS) AF: 0.0356 AC: 184 AN: 5170

South Asian (SAS) AF: 0.0408 AC: 197 AN: 4828

European-Finnish (FIN) AF: 0.0614 AC: 651 AN: 10608

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0146 AC: 993 AN: 68010

Other (OTH) AF: 0.0488 AC: 103 AN: 2110

Alfa AF: 0.0195 Hom.: 14

Bravo AF: 0.0506

Asia WGS AF: 0.0370 AC: 127 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10517830; hg19: chr4-63706224;