rs11015939

Variant names:

• chr10-18729013-G-A
• rs11015939
• ENST00000654305.2:n.104-17676G>A

Variant summary

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

The ENST00000654305.2(ENSG00000234244):​n.104-17676G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 151,952 control chromosomes in the GnomAD database, including 2,379 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 0.17 (2379 hom., cov: 31)
• Consequence: ENSG00000234244 ENST00000654305.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540
• Publications: 1 publications found

Genes affected

ENSG00000234244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376440	XR_930720.2	n.51+18652G>A		intron_variant	Intron 1 of 4
LOC105376440	XR_930721.2	n.69-17676G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234244	ENST00000654305.2	n.104-17676G>A		intron_variant	Intron 1 of 2
ENSG00000234244	ENST00000654415.1	n.79-3403G>A		intron_variant	Intron 1 of 4
ENSG00000234244	ENST00000723466.1	n.53+18652G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25839 AN: 151834 Hom.: 2377 Cov.: 31

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.170 AC: 25851 AN: 151952 Hom.: 2379 Cov.: 31 AF XY: 0.170 AC XY: 12591 AN XY: 74272

African (AFR) AF: 0.0966 AC: 4004 AN: 41462

American (AMR) AF: 0.166 AC: 2534 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 730 AN: 3464

East Asian (EAS) AF: 0.233 AC: 1202 AN: 5156

South Asian (SAS) AF: 0.127 AC: 611 AN: 4808

European-Finnish (FIN) AF: 0.201 AC: 2130 AN: 10572

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14009 AN: 67928

Other (OTH) AF: 0.165 AC: 346 AN: 2102

Alfa AF: 0.194 Hom.: 1535

Bravo AF: 0.165

Asia WGS AF: 0.182 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.86
DANN	Benign	0.32
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs11015939; hg19: chr10-19017942;