2-156890146-T-C

Variant names:

• chr2-156890146-T-C
• rs295791
• ENST00000670545.1:n.3794T>C

Variant summary

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

The ENST00000670545.1(ENSG00000287048):​n.3794T>C 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 0.991 in 151,766 control chromosomes in the GnomAD database, including 74,514 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 0.99 (74514 hom., cov: 32)
• Consequence: ENSG00000287048 ENST00000670545.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 3 publications found

Genes affected

ENSG00000287048 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670545.1. 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
	ENSG00000287048	ENST00000670545.1		n.3794T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000287048	ENST00000762467.1		n.194+3584T>C		intron	N/A
	ENSG00000287048	ENST00000762468.1		n.242+3584T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.991 AC: 150264 AN: 151648 Hom.: 74458 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.997

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.990

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

GnomAD4 genome AF: 0.991 AC: 150379 AN: 151766 Hom.: 74514 Cov.: 32 AF XY: 0.991 AC XY: 73527 AN XY: 74170

African (AFR) AF: 0.968 AC: 40153 AN: 41468

American (AMR) AF: 0.997 AC: 15144 AN: 15188

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3464 AN: 3464

East Asian (EAS) AF: 1.00 AC: 5106 AN: 5106

South Asian (SAS) AF: 1.00 AC: 4822 AN: 4822

European-Finnish (FIN) AF: 1.00 AC: 10616 AN: 10616

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 67782 AN: 67790

Other (OTH) AF: 0.991 AC: 2086 AN: 2106

Alfa AF: 0.994 Hom.: 9138

Bravo AF: 0.990

Asia WGS AF: 0.999 AC: 3473 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.8
DANN	Benign	0.47
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs295791; hg19: chr2-157746658;