2-120581008-T-C

Variant names:

• chr2-120581008-T-C
• rs1880542
• ENST00000825040.1:n.801T>C

Variant summary

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

The ENST00000825040.1(ENSG00000307314):​n.801T>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 0.577 in 152,076 control chromosomes in the GnomAD database, including 25,565 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 0.58 (25565 hom., cov: 33)
• Consequence: ENSG00000307314 ENST00000825040.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 7 publications found

Genes affected

ENSG00000307314 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000825040.1. 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
	ENSG00000307314	ENST00000825040.1		n.801T>C		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87590 AN: 151958 Hom.: 25527 Cov.: 33

Gnomad AFR AF: 0.649

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.577 AC: 87679 AN: 152076 Hom.: 25565 Cov.: 33 AF XY: 0.576 AC XY: 42797 AN XY: 74328

African (AFR) AF: 0.649 AC: 26944 AN: 41486

American (AMR) AF: 0.584 AC: 8921 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2180 AN: 3468

East Asian (EAS) AF: 0.676 AC: 3484 AN: 5156

South Asian (SAS) AF: 0.656 AC: 3162 AN: 4822

European-Finnish (FIN) AF: 0.455 AC: 4802 AN: 10562

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36232 AN: 67986

Other (OTH) AF: 0.592 AC: 1251 AN: 2114

Alfa AF: 0.524 Hom.: 9867

Bravo AF: 0.588

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	17
DANN	Benign	0.50
PhyloP100		0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1880542;

hg19: chr2-121338584;

COSMIC: COSV68619447;