rs10491370

Variant names:

• chr5-54961984-C-A
• rs10491370

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 0.191 in 152,040 control chromosomes in the GnomAD database, including 3,283 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 0.19 (3283 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.600
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.191 AC: 28992 AN: 151920 Hom.: 3287 Cov.: 31

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.191 AC: 28981 AN: 152040 Hom.: 3283 Cov.: 31 AF XY: 0.197 AC XY: 14621 AN XY: 74300

African (AFR) AF: 0.0662 AC: 2747 AN: 41506

American (AMR) AF: 0.211 AC: 3226 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 657 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1384 AN: 5168

South Asian (SAS) AF: 0.327 AC: 1570 AN: 4796

European-Finnish (FIN) AF: 0.283 AC: 2981 AN: 10542

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15877 AN: 67962

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.226 Hom.: 2735

Bravo AF: 0.178

Asia WGS AF: 0.244 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.96
DANN	Benign	0.40
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10491370; hg19: chr5-54257812;