rs10493386

Variant names:

• chr1-65756073-A-C
• rs10493386

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 0.0699 in 152,264 control chromosomes in the GnomAD database, including 760 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 0.070 (760 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 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: 0.0699 AC: 10629 AN: 152146 Hom.: 759 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.0760

Gnomad FIN AF: 0.00744

Gnomad MID AF: 0.0223

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0699 AC: 10649 AN: 152264 Hom.: 760 Cov.: 32 AF XY: 0.0694 AC XY: 5170 AN XY: 74458

Gnomad4 AFR AF: 0.168 AC: 0.167742 AN: 0.167742

Gnomad4 AMR AF: 0.0934 AC: 0.0934231 AN: 0.0934231

Gnomad4 ASJ AF: 0.00663 AC: 0.00662824 AN: 0.00662824

Gnomad4 EAS AF: 0.158 AC: 0.157854 AN: 0.157854

Gnomad4 SAS AF: 0.0756 AC: 0.0756007 AN: 0.0756007

Gnomad4 FIN AF: 0.00744 AC: 0.00743879 AN: 0.00743879

Gnomad4 NFE AF: 0.0120 AC: 0.0119961 AN: 0.0119961

Gnomad4 OTH AF: 0.0686 AC: 0.0685904 AN: 0.0685904

Alfa AF: 0.0312 Hom.: 105

Bravo AF: 0.0814

Asia WGS AF: 0.152 AC: 525 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	18
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10493386; hg19: chr1-66221756;