2-85938320-T-C

Variant names:

• chr2-85938320-T-C
• rs11691934
• ENST00000822158.1:n.*43T>C

Variant summary

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

The ENST00000822158.1(ENSG00000306952):​n.*43T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,978 control chromosomes in the GnomAD database, including 30,594 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 0.63 (30594 hom., cov: 31)
• Consequence: ENSG00000306952 ENST00000822158.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 8 publications found

Genes affected

ENSG00000306952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822158.1. 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
	ENSG00000306952	ENST00000822158.1		n.*43T>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96180 AN: 151860 Hom.: 30575 Cov.: 31

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.633 AC: 96246 AN: 151978 Hom.: 30594 Cov.: 31 AF XY: 0.635 AC XY: 47155 AN XY: 74288

African (AFR) AF: 0.593 AC: 24571 AN: 41404

American (AMR) AF: 0.684 AC: 10440 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2094 AN: 3470

East Asian (EAS) AF: 0.715 AC: 3695 AN: 5170

South Asian (SAS) AF: 0.652 AC: 3139 AN: 4818

European-Finnish (FIN) AF: 0.658 AC: 6940 AN: 10542

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43338 AN: 67990

Other (OTH) AF: 0.637 AC: 1341 AN: 2106

Alfa AF: 0.637 Hom.: 98135

Bravo AF: 0.638

Asia WGS AF: 0.645 AC: 2242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.017
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11691934; hg19: chr2-86165443;