rs10512539

Variant names:

• chr17-70498167-T-C
• rs10512539
• ENST00000785193.1:n.477-3876T>C

Variant summary

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

The ENST00000785193.1(ENSG00000302248):​n.477-3876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,062 control chromosomes in the GnomAD database, including 3,555 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 0.19 (3555 hom., cov: 32)
• Consequence: ENSG00000302248 ENST00000785193.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638
• Publications: 2 publications found

Genes affected

ENSG00000302248 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904100	XR_007065977.1	n.79-3876T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302248	ENST00000785193.1	n.477-3876T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29581 AN: 151942 Hom.: 3551 Cov.: 32

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.0959

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.195 AC: 29592 AN: 152062 Hom.: 3555 Cov.: 32 AF XY: 0.199 AC XY: 14757 AN XY: 74338

African (AFR) AF: 0.124 AC: 5152 AN: 41518

American (AMR) AF: 0.272 AC: 4141 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3464

East Asian (EAS) AF: 0.592 AC: 3057 AN: 5166

South Asian (SAS) AF: 0.336 AC: 1617 AN: 4814

European-Finnish (FIN) AF: 0.0959 AC: 1017 AN: 10602

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13095 AN: 67936

Other (OTH) AF: 0.202 AC: 425 AN: 2108

Alfa AF: 0.182 Hom.: 329

Bravo AF: 0.206

Asia WGS AF: 0.437 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs10512539; hg19: chr17-68494308;