ENST00000689293.2:n.298C>G

Variant names:

• chr1-156503322-C-G
• rs12136856
• ENST00000689293.2:n.298C>G

Variant summary

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

The ENST00000689293.2(ENSG00000288835):​n.298C>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 0.552 in 151,848 control chromosomes in the GnomAD database, including 25,042 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 0.55 (25042 hom., cov: 30)
• Consequence: ENSG00000288835 ENST00000689293.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 20 publications found

Genes affected

ENSG00000288835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.716 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
ENSG00000288835	ENST00000689293.2	n.298C>G		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000303589	ENST00000795918.1	n.102G>C		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000303589	ENST00000795919.1	n.47G>C		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.553 AC: 83842 AN: 151730 Hom.: 25032 Cov.: 30

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.552 AC: 83870 AN: 151848 Hom.: 25042 Cov.: 30 AF XY: 0.553 AC XY: 41065 AN XY: 74208

African (AFR) AF: 0.302 AC: 12500 AN: 41400

American (AMR) AF: 0.600 AC: 9160 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2294 AN: 3466

East Asian (EAS) AF: 0.736 AC: 3782 AN: 5142

South Asian (SAS) AF: 0.682 AC: 3268 AN: 4794

European-Finnish (FIN) AF: 0.570 AC: 6020 AN: 10562

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44853 AN: 67904

Other (OTH) AF: 0.618 AC: 1301 AN: 2104

Alfa AF: 0.485 Hom.: 1579

Bravo AF: 0.541

Asia WGS AF: 0.696 AC: 2422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	9.3
DANN	Benign	0.76
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs12136856; hg19: chr1-156473114;