rs9419596

Variant names:

• chr10-131616301-C-T
• rs9419596

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 0.461 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.221 AC: 9157 AN: 41454

American (AMR) AF: 0.399 AC: 6097 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2070 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5164

South Asian (SAS) AF: 0.317 AC: 1529 AN: 4818

European-Finnish (FIN) AF: 0.665 AC: 7021 AN: 10558

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41111 AN: 67936

Other (OTH) AF: 0.485 AC: 1022 AN: 2108

Alfa AF: 0.548 Hom.: 88456

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
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs9419596; hg19: chr10-133448637;