rs10502575

Variant names:

• chr18-31756628-A-G
• rs10502575
• ENST00000723809.1:n.1000-5511A>G

Variant summary

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

The ENST00000723809.1(ENSG00000293306):​n.1000-5511A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152,266 control chromosomes in the GnomAD database, including 694 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 0.066 (694 hom., cov: 32)
• Consequence: ENSG00000293306 ENST00000723809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 7 publications found

Genes affected

ENSG00000293306 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
ENSG00000293306	ENST00000723809.1	n.1000-5511A>G		intron_variant	Intron 1 of 2
ENSG00000293306	ENST00000723810.1	n.1017-4207A>G		intron_variant	Intron 1 of 1
ENSG00000293306	ENST00000723811.1	n.319-4207A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10051 AN: 152148 Hom.: 687 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0325

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0261

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0636

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

GnomAD4 genome AF: 0.0661 AC: 10069 AN: 152266 Hom.: 694 Cov.: 32 AF XY: 0.0641 AC XY: 4771 AN XY: 74470

African (AFR) AF: 0.179 AC: 7419 AN: 41528

American (AMR) AF: 0.0324 AC: 496 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0251 AC: 87 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0263 AC: 127 AN: 4830

European-Finnish (FIN) AF: 0.0202 AC: 214 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0229 AC: 1559 AN: 68022

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0367 Hom.: 382

Bravo AF: 0.0714

Asia WGS AF: 0.0200 AC: 71 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.35
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10502575; hg19: chr18-29336591;