2-233774392-C-T

Variant names:

• chr2-233774392-C-T
• rs1500482
• ENST00000755739.1:n.310G>A

Variant summary

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

The ENST00000755739.1(ENSG00000298478):​n.310G>A 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 0.8 in 152,090 control chromosomes in the GnomAD database, including 48,779 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 0.80 (48779 hom., cov: 31)
• Consequence: ENSG00000298478 ENST00000755739.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 10 publications found

Genes affected

ENSG00000298478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.861 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
ENSG00000298478	ENST00000755739.1	n.310G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121628 AN: 151972 Hom.: 48742 Cov.: 31

Gnomad AFR AF: 0.803

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.882

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.800 AC: 121722 AN: 152090 Hom.: 48779 Cov.: 31 AF XY: 0.806 AC XY: 59882 AN XY: 74340

African (AFR) AF: 0.803 AC: 33326 AN: 41482

American (AMR) AF: 0.770 AC: 11769 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2417 AN: 3468

East Asian (EAS) AF: 0.882 AC: 4555 AN: 5162

South Asian (SAS) AF: 0.827 AC: 3982 AN: 4816

European-Finnish (FIN) AF: 0.913 AC: 9676 AN: 10602

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53459 AN: 67970

Other (OTH) AF: 0.767 AC: 1622 AN: 2114

Alfa AF: 0.783 Hom.: 72889

Bravo AF: 0.788

Asia WGS AF: 0.842 AC: 2927 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.61
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1500482; hg19: chr2-234683038;