rs10515982

Variant names:

• chr18-60757156-A-G
• rs10515982
• ENST00000591869.1:n.175+14780T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-60757156-A-G
• chr18-60757156-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000591869.1(ENSG00000267098):​n.175+14780T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 151,788 control chromosomes in the GnomAD database, including 713 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 (713 hom., cov: 31)
• Consequence: ENSG00000267098 ENST00000591869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

ENSG00000267098 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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+14780T>C		intron_variant	Intron 4 of 7	4
ENSG00000267098	ENST00000655645.1	n.111+14780T>C		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9225 AN: 151672 Hom.: 703 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0394

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.0222

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.00274

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.0605

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

GnomAD4 genome AF: 0.0611 AC: 9269 AN: 151788 Hom.: 713 Cov.: 31 AF XY: 0.0596 AC XY: 4420 AN XY: 74210

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0393

Gnomad4 ASJ AF: 0.0168

Gnomad4 EAS AF: 0.0223

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.00274

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.0598

Alfa AF: 0.00945 Hom.: 7

Bravo AF: 0.0701

Asia WGS AF: 0.0340 AC: 119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.18
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515982; hg19: chr18-58424389;