rs10493518

Variant names:

• chr1-73394948-G-A
• rs10493518
• ENST00000729649.1:n.85-52429C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-73394948-G-A
• chr1-73394948-G-T

Variant summary

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

The ENST00000729649.1(ENSG00000295376):​n.85-52429C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,940 control chromosomes in the GnomAD database, including 15,852 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 0.45 (15852 hom., cov: 32)
• Consequence: ENSG00000295376 ENST00000729649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.398
• Publications: 2 publications found

Genes affected

ENSG00000295376 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729649.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295376	ENST00000729649.1		n.85-52429C>T		intron	N/A
	ENSG00000295376	ENST00000729650.1		n.85-52429C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68246 AN: 151822 Hom.: 15852 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.449 AC: 68268 AN: 151940 Hom.: 15852 Cov.: 32 AF XY: 0.451 AC XY: 33486 AN XY: 74254

African (AFR) AF: 0.383 AC: 15864 AN: 41448

American (AMR) AF: 0.363 AC: 5535 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3472

East Asian (EAS) AF: 0.767 AC: 3956 AN: 5156

South Asian (SAS) AF: 0.542 AC: 2611 AN: 4820

European-Finnish (FIN) AF: 0.467 AC: 4924 AN: 10552

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32182 AN: 67924

Other (OTH) AF: 0.441 AC: 928 AN: 2106

Alfa AF: 0.445 Hom.: 1980

Bravo AF: 0.437

Asia WGS AF: 0.609 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.6
DANN	Benign	0.56
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10493518; hg19: chr1-73860631; COSMIC: COSV59956035;