rs11003137

Variant names:

• chr10-52780137-G-A
• rs11003137
• ENST00000816733.1:n.504+594G>A

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.504+594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,112 control chromosomes in the GnomAD database, including 1,851 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 0.14 (1851 hom., cov: 31)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.917
• Publications: 8 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378306	XR_945963.2	n.386+594G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306279	ENST00000816733.1	n.504+594G>A		intron_variant	Intron 1 of 3
ENSG00000306279	ENST00000816734.1	n.381+594G>A		intron_variant	Intron 1 of 2
ENSG00000306279	ENST00000816735.1	n.97+1086G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21948 AN: 151994 Hom.: 1857 Cov.: 31

Gnomad AFR AF: 0.0556

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.144 AC: 21934 AN: 152112 Hom.: 1851 Cov.: 31 AF XY: 0.144 AC XY: 10678 AN XY: 74346

African (AFR) AF: 0.0555 AC: 2305 AN: 41528

American (AMR) AF: 0.118 AC: 1807 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3472

East Asian (EAS) AF: 0.160 AC: 823 AN: 5128

South Asian (SAS) AF: 0.236 AC: 1139 AN: 4818

European-Finnish (FIN) AF: 0.166 AC: 1754 AN: 10572

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13143 AN: 67982

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.174 Hom.: 1773

Bravo AF: 0.133

Asia WGS AF: 0.176 AC: 612 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs11003137; hg19: chr10-54539897;