2-237235160-G-T

Variant names:

• chr2-237235160-G-T
• rs4490127
• ENST00000796744.1:n.417G>T

Variant summary

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

The ENST00000796744.1(ENSG00000224132):​n.417G>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 0.615 in 151,934 control chromosomes in the GnomAD database, including 30,929 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 0.61 (30929 hom., cov: 30)
• Consequence: ENSG00000224132 ENST00000796744.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 2 publications found

Genes affected

ENSG00000224132 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000796744.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000224132	ENST00000796744.1		n.417G>T		non_coding_transcript_exon	Exon 5 of 7
	ENSG00000224132	ENST00000796751.1		n.870G>T		non_coding_transcript_exon	Exon 4 of 6
	ENSG00000224132	ENST00000796757.1		n.182G>T		non_coding_transcript_exon	Exon 2 of 4

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93320 AN: 151814 Hom.: 30869 Cov.: 30

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.615 AC: 93438 AN: 151934 Hom.: 30929 Cov.: 30 AF XY: 0.609 AC XY: 45218 AN XY: 74230

African (AFR) AF: 0.880 AC: 36491 AN: 41478

American (AMR) AF: 0.547 AC: 8351 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1897 AN: 3466

East Asian (EAS) AF: 0.516 AC: 2656 AN: 5148

South Asian (SAS) AF: 0.565 AC: 2715 AN: 4806

European-Finnish (FIN) AF: 0.432 AC: 4549 AN: 10520

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35012 AN: 67944

Other (OTH) AF: 0.618 AC: 1305 AN: 2110

Alfa AF: 0.543 Hom.: 94496

Bravo AF: 0.631

Asia WGS AF: 0.590 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.56
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs4490127; hg19: chr2-238143803;