rs11042937

Variant names:

• chr11-10723847-G-T
• rs11042937
• ENST00000760187.1:n.161+5284C>A

Variant summary

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

The ENST00000760187.1(ENSG00000299059):​n.161+5284C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,116 control chromosomes in the GnomAD database, including 27,403 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 0.59 (27403 hom., cov: 33)
• Consequence: ENSG00000299059 ENST00000760187.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 14 publications found

Genes affected

ENSG00000299059 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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
ENSG00000299059	ENST00000760187.1	n.161+5284C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89438 AN: 151998 Hom.: 27352 Cov.: 33

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.488

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.589 AC: 89546 AN: 152116 Hom.: 27403 Cov.: 33 AF XY: 0.588 AC XY: 43746 AN XY: 74356

African (AFR) AF: 0.727 AC: 30177 AN: 41504

American (AMR) AF: 0.683 AC: 10452 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4310 AN: 5178

South Asian (SAS) AF: 0.584 AC: 2819 AN: 4828

European-Finnish (FIN) AF: 0.464 AC: 4896 AN: 10554

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.488 AC: 33196 AN: 67976

Other (OTH) AF: 0.591 AC: 1248 AN: 2112

Alfa AF: 0.530 Hom.: 88217

Bravo AF: 0.617

Asia WGS AF: 0.667 AC: 2317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.037
DANN	Benign	0.82
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11042937; hg19: chr11-10745394;