2-112788290-C-T

Variant names:

• chr2-112788290-C-T
• rs6722023
• ENST00000762716.1:n.1692C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000762716.1(ENSG00000299339):​n.1692C>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 0.0044 in 151,958 control chromosomes in the GnomAD database, including 1 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 0.0044 (1 hom., cov: 30)
• Consequence: ENSG00000299339 ENST00000762716.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140
• Publications: 2 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762716.1. 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
	ENSG00000299339	ENST00000762716.1		n.1692C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000299339	ENST00000762706.1		n.404+17394C>T		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+17394C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00440 AC: 668 AN: 151840 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.00571

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000854

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00719

Gnomad OTH AF: 0.00673

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

GnomAD4 genome AF: 0.00440 AC: 668 AN: 151958 Hom.: 1 Cov.: 30 AF XY: 0.00401 AC XY: 298 AN XY: 74268

African (AFR) AF: 0.00157 AC: 65 AN: 41452

American (AMR) AF: 0.00570 AC: 87 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4806

European-Finnish (FIN) AF: 0.000854 AC: 9 AN: 10540

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00719 AC: 489 AN: 67964

Other (OTH) AF: 0.00666 AC: 14 AN: 2102

Alfa AF: 0.00426 Hom.: 0

Bravo AF: 0.00481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.41
DANN	Benign	0.30
PhyloP100		0.014

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: rs6722023;

hg19: chr2-113545867;