rs1393491

Variant names:

• chr10-100367390-T-C
• rs1393491

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 0.149 in 152,062 control chromosomes in the GnomAD database, including 1,854 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 0.15 (1854 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

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 = 0.223 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: 0.149 AC: 22637 AN: 151942 Hom.: 1849 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.149 AC: 22655 AN: 152062 Hom.: 1854 Cov.: 32 AF XY: 0.148 AC XY: 10967 AN XY: 74344

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.143

Alfa AF: 0.161 Hom.: 2181

Bravo AF: 0.145

Asia WGS AF: 0.161 AC: 560 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	2.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1393491; hg19: chr10-102127147;