2-157049696-A-G

Variant names:

• chr2-157049696-A-G
• rs1481385
• ENST00000653962.2:n.1014A>G

Variant summary

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

The ENST00000653962.2(ENSG00000286530):​n.1014A>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 0.862 in 152,192 control chromosomes in the GnomAD database, including 57,069 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 0.86 (57069 hom., cov: 32)
• Consequence: ENSG00000286530 ENST00000653962.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.236
• Publications: 2 publications found

Genes affected

ENSG00000286530 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653962.2. 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
	ENSG00000286530	ENST00000653962.2		n.1014A>G		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.862 AC: 131098 AN: 152074 Hom.: 57021 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.845

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

GnomAD4 genome AF: 0.862 AC: 131201 AN: 152192 Hom.: 57069 Cov.: 32 AF XY: 0.863 AC XY: 64192 AN XY: 74400

African (AFR) AF: 0.962 AC: 39969 AN: 41562

American (AMR) AF: 0.894 AC: 13666 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3470

East Asian (EAS) AF: 0.636 AC: 3285 AN: 5162

South Asian (SAS) AF: 0.790 AC: 3807 AN: 4816

European-Finnish (FIN) AF: 0.887 AC: 9397 AN: 10596

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55653 AN: 67988

Other (OTH) AF: 0.845 AC: 1785 AN: 2112

Alfa AF: 0.834 Hom.: 65913

Bravo AF: 0.867

Asia WGS AF: 0.766 AC: 2665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.40
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1481385; hg19: chr2-157906208;