ENST00000834606.1:n.91-3369A>G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376621	XR_931176.3	n.91-3369A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308500	ENST00000834606.1	n.91-3369A>G		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834607.1	n.136-3369A>G		intron_variant	Intron 1 of 3
ENSG00000308500	ENST00000834608.1	n.92-3369A>G		intron_variant	Intron 1 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs941940; hg19: chr11-33924787;