rs11003134

Variant names:

• chr10-52778399-C-A
• rs11003134
• ENST00000816985.1:n.377G>T

Variant summary

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

The ENST00000816985.1(ENSG00000306325):​n.377G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,206 control chromosomes in the GnomAD database, including 1,383 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 0.13 (1383 hom., cov: 32)
• Consequence: ENSG00000306325 ENST00000816985.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 10 publications found

Genes affected

ENSG00000306325 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.142 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
ENSG00000306325	ENST00000816985.1	n.377G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20429 AN: 152088 Hom.: 1382 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.134 AC: 20440 AN: 152206 Hom.: 1383 Cov.: 32 AF XY: 0.134 AC XY: 9998 AN XY: 74420

African (AFR) AF: 0.113 AC: 4709 AN: 41546

American (AMR) AF: 0.134 AC: 2050 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 655 AN: 3466

East Asian (EAS) AF: 0.0895 AC: 463 AN: 5174

South Asian (SAS) AF: 0.138 AC: 664 AN: 4828

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10594

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9845 AN: 67998

Other (OTH) AF: 0.145 AC: 305 AN: 2110

Alfa AF: 0.142 Hom.: 2727

Bravo AF: 0.134

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.47
DANN	Benign	0.58
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs11003134; hg19: chr10-54538159;