2-85335049-C-T

Variant names:

• chr2-85335049-C-T
• rs3923229
• ENST00000825767.1:n.211-6751C>T

Variant summary

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

The ENST00000825767.1(ENSG00000307411):​n.211-6751C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,178 control chromosomes in the GnomAD database, including 50,636 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 0.81 (50636 hom., cov: 32)
• Consequence: ENSG00000307411 ENST00000825767.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 17 publications found

Genes affected

ENSG00000307411 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307411	ENST00000825767.1	n.211-6751C>T		intron_variant	Intron 1 of 1
ENSG00000307411	ENST00000825768.1	n.196-5673C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123291 AN: 152060 Hom.: 50595 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.799

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

GnomAD4 genome AF: 0.811 AC: 123390 AN: 152178 Hom.: 50636 Cov.: 32 AF XY: 0.816 AC XY: 60717 AN XY: 74370

African (AFR) AF: 0.926 AC: 38463 AN: 41550

American (AMR) AF: 0.830 AC: 12692 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.747 AC: 2593 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4842 AN: 5170

South Asian (SAS) AF: 0.925 AC: 4466 AN: 4830

European-Finnish (FIN) AF: 0.763 AC: 8070 AN: 10572

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49688 AN: 67976

Other (OTH) AF: 0.801 AC: 1689 AN: 2108

Alfa AF: 0.759 Hom.: 190155

Bravo AF: 0.819

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.47
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs3923229; hg19: chr2-85562172;