rs10493383

Variant names:

• chr1-65709249-C-G
• rs10493383
• ENST00000646875.1:n.346-1564C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646875.1(ENSG00000285079):​n.346-1564C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0112 in 152,282 control chromosomes in the GnomAD database, including 51 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 0.011 (51 hom., cov: 31)
• Consequence: ENSG00000285079 ENST00000646875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

Genes affected

ENSG00000285079 (HGNC:):

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 = 0.0886 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
ENSG00000285079	ENST00000646875.1	n.346-1564C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0111 AC: 1691 AN: 152164 Hom.: 48 Cov.: 31

Gnomad AFR AF: 0.00746

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00537

Gnomad ASJ AF: 0.0222

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00225

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0112 AC: 1707 AN: 152282 Hom.: 51 Cov.: 31 AF XY: 0.0135 AC XY: 1007 AN XY: 74474

Gnomad4 AFR AF: 0.00779

Gnomad4 AMR AF: 0.00536

Gnomad4 ASJ AF: 0.0222

Gnomad4 EAS AF: 0.0668

Gnomad4 SAS AF: 0.0959

Gnomad4 FIN AF: 0.0212

Gnomad4 NFE AF: 0.00225

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00603 Hom.: 2

Bravo AF: 0.00772

Asia WGS AF: 0.109 AC: 378 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	0.33
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: rs10493383; hg19: chr1-66174932;