2-127225069-A-T

Variant names:

• chr2-127225069-A-T
• rs7567389
• ENST00000829312.1:n.287A>T

Variant summary

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

The ENST00000829312.1(ENSG00000307844):​n.287A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 151,998 control chromosomes in the GnomAD database, including 34,541 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 0.67 (34541 hom., cov: 31)
• Consequence: ENSG00000307844 ENST00000829312.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.643
• Publications: 11 publications found

Genes affected

ENSG00000307844 (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 (EAS) allele frequency at 95% confidence interval = 0.883 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
ENSG00000307844	ENST00000829312.1	n.287A>T		non_coding_transcript_exon_variant	Exon 2 of 4
ENSG00000307844	ENST00000829313.1	n.229A>T		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000307844	ENST00000829314.1	n.263A>T		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101864 AN: 151880 Hom.: 34495 Cov.: 31

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.671 AC: 101971 AN: 151998 Hom.: 34541 Cov.: 31 AF XY: 0.676 AC XY: 50206 AN XY: 74312

African (AFR) AF: 0.626 AC: 25916 AN: 41424

American (AMR) AF: 0.770 AC: 11757 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3470

East Asian (EAS) AF: 0.905 AC: 4677 AN: 5170

South Asian (SAS) AF: 0.600 AC: 2885 AN: 4806

European-Finnish (FIN) AF: 0.720 AC: 7612 AN: 10576

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44629 AN: 67964

Other (OTH) AF: 0.679 AC: 1433 AN: 2112

Alfa AF: 0.590 Hom.: 1899

Bravo AF: 0.677

Asia WGS AF: 0.785 AC: 2724 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	0.17
DANN	Benign	0.34
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs7567389; hg19: chr2-127982645;