2-62294109-G-T

Variant names:

• chr2-62294109-G-T
• rs4672495
• ENST00000807679.1:n.302+18522G>T

Variant summary

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

The ENST00000807679.1(ENSG00000228541):​n.302+18522G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,194 control chromosomes in the GnomAD database, including 44,521 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 0.76 (44521 hom., cov: 33)
• Consequence: ENSG00000228541 ENST00000807679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.860
• Publications: 19 publications found

Genes affected

ENSG00000228541 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807679.1. 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
	ENSG00000228541	ENST00000807679.1		n.302+18522G>T		intron	N/A
	ENSG00000228541	ENST00000807680.1		n.298+18522G>T		intron	N/A
	ENSG00000228541	ENST00000807681.1		n.282+18522G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114946 AN: 152076 Hom.: 44449 Cov.: 33

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.756 AC: 115086 AN: 152194 Hom.: 44521 Cov.: 33 AF XY: 0.756 AC XY: 56240 AN XY: 74390

African (AFR) AF: 0.933 AC: 38810 AN: 41578

American (AMR) AF: 0.735 AC: 11245 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3472

East Asian (EAS) AF: 0.832 AC: 4289 AN: 5156

South Asian (SAS) AF: 0.751 AC: 3614 AN: 4814

European-Finnish (FIN) AF: 0.674 AC: 7135 AN: 10588

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45328 AN: 67964

Other (OTH) AF: 0.738 AC: 1562 AN: 2116

Alfa AF: 0.696 Hom.: 157928

Bravo AF: 0.767

Asia WGS AF: 0.787 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.79
PhyloP100		0.86

Splicing

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

Other links and lift over

dbSNP: rs4672495; hg19: chr2-62521244;