2-154692047-T-G

Variant names:

• chr2-154692047-T-G
• rs3111037
• ENST00000654516.1:n.999A>C

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000287900 ENST00000654516.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581
• Publications: 4 publications found

Genes affected

ENSG00000287900 (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 = 0.594 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287900	ENST00000654516.1	n.999A>C		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000287900	ENST00000662205.1	n.2891A>C		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000287900	ENST00000803273.1	n.1275A>C		non_coding_transcript_exon_variant	Exon 3 of 5

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

African (AFR) AF: 0.600 AC: 24869 AN: 41438

American (AMR) AF: 0.500 AC: 7630 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3468

East Asian (EAS) AF: 0.366 AC: 1887 AN: 5156

South Asian (SAS) AF: 0.531 AC: 2557 AN: 4814

European-Finnish (FIN) AF: 0.659 AC: 6954 AN: 10550

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.562 AC: 38176 AN: 67954

Other (OTH) AF: 0.520 AC: 1096 AN: 2108

Alfa AF: 0.552 Hom.: 75079

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
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs3111037; hg19: chr2-155548559;