rs10518339

Variant names:

• chr4-119858047-G-A
• rs10518339

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 0.0676 in 152,196 control chromosomes in the GnomAD database, including 776 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 0.068 (776 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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: 0.0675 AC: 10267 AN: 152080 Hom.: 775 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0331

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00683

Gnomad FIN AF: 0.00339

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0181

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0676 AC: 10281 AN: 152196 Hom.: 776 Cov.: 32 AF XY: 0.0653 AC XY: 4857 AN XY: 74416

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0438

Gnomad4 ASJ AF: 0.0331

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00663

Gnomad4 FIN AF: 0.00339

Gnomad4 NFE AF: 0.0181

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0439 Hom.: 60

Bravo AF: 0.0771

Asia WGS AF: 0.0150 AC: 51 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.54
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10518339; hg19: chr4-120779202;