rs10502578

Variant names:

• chr18-31795124-G-A
• rs10502578
• ENST00000719560.1:n.36+7370C>T

Variant summary

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

The ENST00000719560.1(ENSG00000293872):​n.36+7370C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,238 control chromosomes in the GnomAD database, including 528 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 0.082 (528 hom., cov: 32)
• Consequence: ENSG00000293872 ENST00000719560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0880
• Publications: 1 publications found

Genes affected

ENSG00000293872 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0904 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
ENSG00000293872	ENST00000719560.1	n.36+7370C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12474 AN: 152120 Hom.: 529 Cov.: 32

Gnomad AFR AF: 0.0797

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0723

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.0768

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0819 AC: 12475 AN: 152238 Hom.: 528 Cov.: 32 AF XY: 0.0814 AC XY: 6062 AN XY: 74430

African (AFR) AF: 0.0797 AC: 3309 AN: 41536

American (AMR) AF: 0.0722 AC: 1104 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.0480 AC: 248 AN: 5166

South Asian (SAS) AF: 0.0977 AC: 471 AN: 4820

European-Finnish (FIN) AF: 0.0768 AC: 814 AN: 10604

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.0851 AC: 5786 AN: 68028

Other (OTH) AF: 0.0928 AC: 196 AN: 2112

Alfa AF: 0.0867 Hom.: 1094

Bravo AF: 0.0814

Asia WGS AF: 0.0800 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	9.5
DANN	Benign	0.56
PhyloP100		0.088

Splicing

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

Other links and lift over

dbSNP: rs10502578; hg19: chr18-29375087;