rs10519394

Variant names:

• chr4-136683454-C-A
• rs10519394

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 0.086 in 152,036 control chromosomes in the GnomAD database, including 650 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 0.086 (650 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.105 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: 0.0861 AC: 13073 AN: 151918 Hom.: 649 Cov.: 32

Gnomad AFR AF: 0.0374

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0962

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.0844

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

GnomAD4 genome AF: 0.0860 AC: 13073 AN: 152036 Hom.: 650 Cov.: 32 AF XY: 0.0871 AC XY: 6475 AN XY: 74304

African (AFR) AF: 0.0373 AC: 1548 AN: 41520

American (AMR) AF: 0.0962 AC: 1467 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0646 AC: 224 AN: 3470

East Asian (EAS) AF: 0.0925 AC: 477 AN: 5156

South Asian (SAS) AF: 0.0918 AC: 443 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1406 AN: 10584

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7305 AN: 67924

Other (OTH) AF: 0.0835 AC: 176 AN: 2108

Alfa AF: 0.0975 Hom.: 1275

Bravo AF: 0.0798

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.21
DANN	Benign	0.61
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10519394; hg19: chr4-137604609;