rs941940

Variant names:

• chr11-33903240-A-G
• rs941940
• ENST00000834606.1:n.91-3369A>G

Variant summary

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

The ENST00000834606.1(ENSG00000308500):​n.91-3369A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,938 control chromosomes in the GnomAD database, including 31,019 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 0.64 (31019 hom., cov: 30)
• Consequence: ENSG00000308500 ENST00000834606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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.91-3369A>G		intron	N/A
	ENSG00000308500	ENST00000834607.1		n.136-3369A>G		intron	N/A
	ENSG00000308500	ENST00000834608.1		n.92-3369A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96778 AN: 151820 Hom.: 30999 Cov.: 30

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.637 AC: 96832 AN: 151938 Hom.: 31019 Cov.: 30 AF XY: 0.633 AC XY: 47039 AN XY: 74260

African (AFR) AF: 0.678 AC: 28082 AN: 41398

American (AMR) AF: 0.548 AC: 8369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.584 AC: 2025 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3058 AN: 5162

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4814

European-Finnish (FIN) AF: 0.668 AC: 7042 AN: 10546

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.640 AC: 43503 AN: 67958

Other (OTH) AF: 0.625 AC: 1317 AN: 2106

Alfa AF: 0.635 Hom.: 39833

Bravo AF: 0.632

Asia WGS AF: 0.520 AC: 1809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.22
PhyloP100		-0.23

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs941940;

hg19: chr11-33924787;