rs10493517

Variant names:

• chr1-73392668-G-A
• rs10493517
• ENST00000729649.1:n.85-50149C>T

Variant summary

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

The ENST00000729649.1(ENSG00000295376):​n.85-50149C>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 151,928 control chromosomes in the GnomAD database, including 15,851 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 (15851 hom., cov: 32)
• Consequence: ENSG00000295376 ENST00000729649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 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
ENSG00000295376	ENST00000729649.1	n.85-50149C>T		intron_variant	Intron 1 of 2
ENSG00000295376	ENST00000729650.1	n.85-50149C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68238 AN: 151808 Hom.: 15850 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.497

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.449 AC: 68262 AN: 151928 Hom.: 15851 Cov.: 32 AF XY: 0.451 AC XY: 33498 AN XY: 74250

African (AFR) AF: 0.383 AC: 15851 AN: 41400

American (AMR) AF: 0.363 AC: 5551 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1669 AN: 3466

East Asian (EAS) AF: 0.767 AC: 3953 AN: 5154

South Asian (SAS) AF: 0.541 AC: 2608 AN: 4818

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: 32183 AN: 67944

Other (OTH) AF: 0.439 AC: 927 AN: 2112

Alfa AF: 0.453 Hom.: 2098

Bravo AF: 0.437

Asia WGS AF: 0.609 AC: 2116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.77
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10493517; hg19: chr1-73858351; COSMIC: COSV59956032;