11-33903176-T-C

Variant names:

• chr11-33903176-T-C
• rs941941
• ENST00000834606.1:n.91-3433T>C

Variant summary

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

The ENST00000834606.1(ENSG00000308500):​n.91-3433T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,006 control chromosomes in the GnomAD database, including 18,519 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 0.49 (18519 hom., cov: 32)
• Consequence: ENSG00000308500 ENST00000834606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 7 publications found

Genes affected

ENSG00000308500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376621	XR_931176.3	n.91-3433T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308500	ENST00000834606.1	n.91-3433T>C		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834607.1	n.136-3433T>C		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834608.1	n.92-3433T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 74989 AN: 151888 Hom.: 18510 Cov.: 32

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.494 AC: 75022 AN: 152006 Hom.: 18519 Cov.: 32 AF XY: 0.491 AC XY: 36467 AN XY: 74284

African (AFR) AF: 0.495 AC: 20528 AN: 41448

American (AMR) AF: 0.445 AC: 6794 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1438 AN: 3468

East Asian (EAS) AF: 0.443 AC: 2295 AN: 5176

South Asian (SAS) AF: 0.459 AC: 2212 AN: 4816

European-Finnish (FIN) AF: 0.528 AC: 5568 AN: 10542

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34498 AN: 67962

Other (OTH) AF: 0.484 AC: 1021 AN: 2108

Alfa AF: 0.497 Hom.: 18985

Bravo AF: 0.489

Asia WGS AF: 0.410 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs941941; hg19: chr11-33924723;