2-154692047-T-G

Position:

• chr2-154692047-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654516.1(ENSG00000287900):​n.999A>C 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 0.564 in 151,962 control chromosomes in the GnomAD database, including 24,538 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 0.56 (24538 hom., cov: 32)
• Consequence: ENST00000654516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654516.1	n.999A>C		non_coding_transcript_exon_variant	3/4
	ENST00000662205.1	n.2891A>C		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85558 AN: 151844 Hom.: 24512 Cov.: 32

Gnomad AFR AF: 0.600

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.564 AC: 85631 AN: 151962 Hom.: 24538 Cov.: 32 AF XY: 0.564 AC XY: 41878 AN XY: 74228

Gnomad4 AFR AF: 0.600

Gnomad4 AMR AF: 0.500

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.520

Alfa AF: 0.547 Hom.: 31718

Bravo AF: 0.551

Asia WGS AF: 0.498 AC: 1734 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.76
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3111037; hg19: chr2-155548559;