rs4368333

Variant names:

• chr2-17849398-C-A
• rs4368333
• ENST00000750479.1:n.92G>T

Variant summary

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

The ENST00000750479.1(ENSG00000297720):​n.92G>T 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 0.49 in 151,928 control chromosomes in the GnomAD database, including 19,120 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 0.49 (19120 hom., cov: 31)
• Consequence: ENSG00000297720 ENST00000750479.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 5 publications found

Genes affected

ENSG00000297720 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267888	XR_939764.2	n.86G>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297720	ENST00000750479.1	n.92G>T		non_coding_transcript_exon_variant	Exon 1 of 4
ENSG00000297720	ENST00000750480.1	n.54G>T		non_coding_transcript_exon_variant	Exon 1 of 5
ENSG00000297720	ENST00000750484.1	n.92G>T		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74318 AN: 151810 Hom.: 19106 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.490 AC: 74370 AN: 151928 Hom.: 19120 Cov.: 31 AF XY: 0.484 AC XY: 35930 AN XY: 74268

African (AFR) AF: 0.433 AC: 17944 AN: 41408

American (AMR) AF: 0.407 AC: 6214 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2170 AN: 3468

East Asian (EAS) AF: 0.0503 AC: 260 AN: 5174

South Asian (SAS) AF: 0.437 AC: 2105 AN: 4814

European-Finnish (FIN) AF: 0.531 AC: 5601 AN: 10540

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38115 AN: 67942

Other (OTH) AF: 0.518 AC: 1095 AN: 2112

Alfa AF: 0.537 Hom.: 71128

Bravo AF: 0.476

Asia WGS AF: 0.245 AC: 860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4368333; hg19: chr2-18030665;