2-208156577-A-G

Variant names:

• chr2-208156577-A-G
• rs796272
• ENST00000728539.1:n.272A>G

Variant summary

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

The ENST00000728539.1(ENSG00000295187):​n.272A>G 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 0.896 in 152,062 control chromosomes in the GnomAD database, including 61,579 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 0.90 (61579 hom., cov: 30)
• Consequence: ENSG00000295187 ENST00000728539.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135
• Publications: 5 publications found

Genes affected

ENSG00000295187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728539.1. 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
	LOC100507443	NR_038437.1		n.252A>G		non_coding_transcript_exon	Exon 3 of 3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295187	ENST00000728539.1		n.272A>G		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000295187	ENST00000728538.1		n.224+19398A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136163 AN: 151944 Hom.: 61525 Cov.: 30

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.901

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

GnomAD4 genome AF: 0.896 AC: 136281 AN: 152062 Hom.: 61579 Cov.: 30 AF XY: 0.891 AC XY: 66247 AN XY: 74320

African (AFR) AF: 0.921 AC: 38210 AN: 41468

American (AMR) AF: 0.822 AC: 12546 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.936 AC: 3251 AN: 3472

East Asian (EAS) AF: 0.551 AC: 2842 AN: 5158

South Asian (SAS) AF: 0.826 AC: 3967 AN: 4804

European-Finnish (FIN) AF: 0.921 AC: 9740 AN: 10574

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.923 AC: 62753 AN: 67998

Other (OTH) AF: 0.900 AC: 1903 AN: 2114

Alfa AF: 0.914 Hom.: 108374

Bravo AF: 0.888

Asia WGS AF: 0.692 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.77
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs796272; hg19: chr2-209021301;