10-18729013-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654305.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234244	ENST00000654305.2		n.104-17676G>A		intron	N/A
	ENSG00000234244	ENST00000654415.1		n.79-3403G>A		intron	N/A
	ENSG00000234244	ENST00000723466.1		n.53+18652G>A		intron	N/A

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 v4.9

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;