rs10515983

Variant names:

• chr18-60759099-T-C
• rs10515983
• ENST00000591869.1:n.175+12837A>G

Variant summary

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

The ENST00000591869.1(ENSG00000267098):​n.175+12837A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 152,112 control chromosomes in the GnomAD database, including 709 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 0.061 (709 hom., cov: 32)
• Consequence: ENSG00000267098 ENST00000591869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.741
• Publications: 1 publications found

Genes affected

ENSG00000267098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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
ENSG00000267098	ENST00000591869.1	n.175+12837A>G		intron_variant	Intron 4 of 7	4
ENSG00000267098	ENST00000655645.1	n.111+12837A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0609 AC: 9257 AN: 151994 Hom.: 699 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0395

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0138

Gnomad OTH AF: 0.0612

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

GnomAD4 genome AF: 0.0612 AC: 9302 AN: 152112 Hom.: 709 Cov.: 32 AF XY: 0.0596 AC XY: 4432 AN XY: 74378

African (AFR) AF: 0.177 AC: 7340 AN: 41516

American (AMR) AF: 0.0393 AC: 599 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3468

East Asian (EAS) AF: 0.0226 AC: 117 AN: 5182

South Asian (SAS) AF: 0.0157 AC: 76 AN: 4826

European-Finnish (FIN) AF: 0.00292 AC: 31 AN: 10630

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0138 AC: 936 AN: 67944

Other (OTH) AF: 0.0605 AC: 128 AN: 2114

Alfa AF: 0.0458 Hom.: 60

Bravo AF: 0.0701

Asia WGS AF: 0.0350 AC: 120 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.34
DANN	Benign	0.50
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10515983; hg19: chr18-58426332;