chr2-112813495-C-G

Variant names:

• chr2-112813495-C-G
• rs12711742
• ENST00000762824.1:n.382G>C

Variant summary

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

The ENST00000762824.1(ENSG00000287937):​n.382G>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 0.866 in 152,196 control chromosomes in the GnomAD database, including 57,220 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 0.87 (57220 hom., cov: 31)
• Consequence: ENSG00000287937 ENST00000762824.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280
• Publications: 4 publications found

Genes affected

ENSG00000287937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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
ENSG00000287937	ENST00000762824.1	n.382G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000287937	ENST00000762825.1	n.288G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000299339	ENST00000762706.1	n.404+42599C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.866 AC: 131724 AN: 152078 Hom.: 57170 Cov.: 31

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.877

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.912

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.873

Gnomad OTH AF: 0.868

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

GnomAD4 genome AF: 0.866 AC: 131828 AN: 152196 Hom.: 57220 Cov.: 31 AF XY: 0.870 AC XY: 64752 AN XY: 74426

African (AFR) AF: 0.813 AC: 33729 AN: 41482

American (AMR) AF: 0.903 AC: 13797 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.877 AC: 3040 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5186 AN: 5190

South Asian (SAS) AF: 0.843 AC: 4073 AN: 4830

European-Finnish (FIN) AF: 0.912 AC: 9683 AN: 10616

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.873 AC: 59386 AN: 68018

Other (OTH) AF: 0.869 AC: 1831 AN: 2108

Alfa AF: 0.864 Hom.: 2878

Bravo AF: 0.864

Asia WGS AF: 0.919 AC: 3196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		0.028

Splicing

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

Other links and lift over

dbSNP: rs12711742; hg19: chr2-113571072;