rs10491404

Variant names:

• chr5-147165893-C-T
• rs10491404

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 0.18 in 152,112 control chromosomes in the GnomAD database, including 3,072 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 0.18 (3072 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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: 0.180 AC: 27351 AN: 151992 Hom.: 3075 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.140

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.180 AC: 27369 AN: 152112 Hom.: 3072 Cov.: 32 AF XY: 0.190 AC XY: 14135 AN XY: 74354

African (AFR) AF: 0.155 AC: 6415 AN: 41508

American (AMR) AF: 0.229 AC: 3494 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 654 AN: 3472

East Asian (EAS) AF: 0.535 AC: 2767 AN: 5174

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4824

European-Finnish (FIN) AF: 0.246 AC: 2598 AN: 10566

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.138 AC: 9373 AN: 67986

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.165 Hom.: 296

Bravo AF: 0.179

Asia WGS AF: 0.377 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs10491404; hg19: chr5-146545456;