rs11031676

Variant names:

• chr11-32264599-C-T
• rs11031676
• ENST00000525689.2:n.123-34238G>A

Variant summary

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

The ENST00000525689.2(ENSG00000293378):​n.123-34238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 152,050 control chromosomes in the GnomAD database, including 3,515 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 0.20 (3515 hom., cov: 32)
• Consequence: ENSG00000293378 ENST00000525689.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 2 publications found

Genes affected

ENSG00000293378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 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
ENSG00000293378	ENST00000525689.2	n.123-34238G>A		intron_variant	Intron 1 of 1	3
ENSG00000293378	ENST00000781589.1	n.75+15186G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30436 AN: 151932 Hom.: 3514 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.0219

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.200 AC: 30438 AN: 152050 Hom.: 3515 Cov.: 32 AF XY: 0.200 AC XY: 14836 AN XY: 74308

African (AFR) AF: 0.131 AC: 5437 AN: 41494

American (AMR) AF: 0.176 AC: 2697 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1197 AN: 3470

East Asian (EAS) AF: 0.0218 AC: 113 AN: 5182

South Asian (SAS) AF: 0.130 AC: 622 AN: 4802

European-Finnish (FIN) AF: 0.245 AC: 2585 AN: 10540

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16921 AN: 67966

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.237 Hom.: 945

Bravo AF: 0.192

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.77
PhyloP100		-0.017

Splicing

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

Other links and lift over

dbSNP: rs11031676; hg19: chr11-32286145;