rs10491370

chr5-54961984-C-A

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 0.191 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.171

Alfa AF: 0.225 Hom.: 2549

Bravo AF: 0.178

Asia WGS AF: 0.244 AC: 846 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	0.96
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491370; hg19: chr5-54257812;