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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834606.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308500	ENST00000834606.1		n.91-3433T>C		intron	N/A
	ENSG00000308500	ENST00000834607.1		n.136-3433T>C		intron	N/A
	ENSG00000308500	ENST00000834608.1		n.92-3433T>C		intron	N/A

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 v4.9

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;