ENST00000849275.1:n.352C>T

Variant names:

• chr2-20135948-G-A
• rs4666360
• ENST00000849275.1:n.352C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000849275.1(ENSG00000234378):​n.352C>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 0.434 in 151,948 control chromosomes in the GnomAD database, including 16,051 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 0.43 (16051 hom., cov: 30)
• Consequence: ENSG00000234378 ENST00000849275.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.517
• Publications: 8 publications found

Genes affected

ENSG00000234378 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234378	ENST00000849275.1		n.352C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000234378	ENST00000849271.1		n.140+147C>T		intron	N/A
	ENSG00000234378	ENST00000849272.1		n.249+147C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65857 AN: 151830 Hom.: 16000 Cov.: 30

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.434 AC: 65980 AN: 151948 Hom.: 16051 Cov.: 30 AF XY: 0.444 AC XY: 32976 AN XY: 74264

African (AFR) AF: 0.603 AC: 24985 AN: 41414

American (AMR) AF: 0.456 AC: 6968 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3466

East Asian (EAS) AF: 0.811 AC: 4191 AN: 5166

South Asian (SAS) AF: 0.569 AC: 2736 AN: 4808

European-Finnish (FIN) AF: 0.380 AC: 4014 AN: 10564

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.304 AC: 20646 AN: 67950

Other (OTH) AF: 0.407 AC: 857 AN: 2108

Alfa AF: 0.344 Hom.: 41065

Bravo AF: 0.447

Asia WGS AF: 0.677 AC: 2351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	0.54
DANN	Benign	0.64
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs4666360; hg19: chr2-20335709;