rs9419596

Variant names:

• chr10-131616301-C-T
• rs9419596

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 0.461 in 151,988 control chromosomes in the GnomAD database, including 18,622 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 0.46 (18622 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.452

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.462 AC: 70132 AN: 151870 Hom.: 18622 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.400

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.461 AC: 70128 AN: 151988 Hom.: 18622 Cov.: 32 AF XY: 0.457 AC XY: 33983 AN XY: 74294

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.399

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.261

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.485

Alfa AF: 0.569 Hom.: 35922

Bravo AF: 0.436

Asia WGS AF: 0.283 AC: 984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9419596; hg19: chr10-133448637;