rs10493386

Variant names:

• chr1-65756073-A-C
• rs10493386
• ENST00000760442.1:n.342+34158T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000760442.1(ENSG00000299098):​n.342+34158T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000299098 ENST00000760442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.21
• Publications: 1 publications found

Genes affected

ENSG00000299098 (HGNC:):

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
ENSG00000299098	ENST00000760442.1	n.342+34158T>G		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.168 AC: 6966 AN: 41528

American (AMR) AF: 0.0934 AC: 1429 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3470

East Asian (EAS) AF: 0.158 AC: 818 AN: 5182

South Asian (SAS) AF: 0.0756 AC: 365 AN: 4828

European-Finnish (FIN) AF: 0.00744 AC: 79 AN: 10620

Middle Eastern (MID) AF: 0.0205 AC: 6 AN: 292

European-Non Finnish (NFE) AF: 0.0120 AC: 816 AN: 68022

Other (OTH) AF: 0.0686 AC: 145 AN: 2114

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
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs10493386; hg19: chr1-66221756;