chr2-118049019-G-T

Variant names:

• chr2-118049019-G-T
• rs6746842
• ENST00000627626.1:n.247-5701G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000627626.1(ENSG00000235066):​n.247-5701G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000235066 ENST00000627626.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 4 publications found

Genes affected

ENSG00000235066 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723413	XR_427162.4	n.261-3568G>T		intron_variant	Intron 2 of 4
LOC102723413	XR_923243.3	n.261-3568G>T		intron_variant	Intron 2 of 3
LOC102723413	XR_923245.3	n.260+3637G>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235066	ENST00000627626.1	n.247-5701G>T		intron_variant	Intron 2 of 2	5
ENSG00000235066	ENST00000627670.3	n.1227-5676G>T		intron_variant	Intron 5 of 5	5
ENSG00000297418	ENST00000747789.1	n.232-3326C>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 967

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.59
PhyloP100		0.054

Splicing

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

Other links and lift over

dbSNP: rs6746842; hg19: chr2-118806595;