rs10517484

Variant names:

• chr4-59837296-A-T
• rs10517484

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 0.604 in 151,422 control chromosomes in the GnomAD database, including 28,407 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 0.60 (28407 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• 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 = 0.727 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: 0.604 AC: 91393 AN: 151306 Hom.: 28383 Cov.: 30

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.604 AC: 91467 AN: 151422 Hom.: 28407 Cov.: 30 AF XY: 0.601 AC XY: 44451 AN XY: 73940

African (AFR) AF: 0.734 AC: 30347 AN: 41350

American (AMR) AF: 0.661 AC: 10005 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1830 AN: 3462

East Asian (EAS) AF: 0.385 AC: 1960 AN: 5094

South Asian (SAS) AF: 0.437 AC: 2098 AN: 4806

European-Finnish (FIN) AF: 0.546 AC: 5743 AN: 10518

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37515 AN: 67734

Other (OTH) AF: 0.570 AC: 1203 AN: 2112

Alfa AF: 0.585 Hom.: 3271

Bravo AF: 0.620

Asia WGS AF: 0.406 AC: 1413 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	0.72
DANN	Benign	0.38
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10517484; hg19: chr4-60703014;