rs2337146

Variant names:

• chr18-48956537-C-T
• rs2337146
• ENST00000754457.1:n.948C>T

Variant summary

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

The ENST00000754457.1(ENSG00000298289):​n.948C>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 0.108 in 152,110 control chromosomes in the GnomAD database, including 1,979 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 0.11 (1979 hom., cov: 32)
• Consequence: ENSG00000298289 ENST00000754457.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 3 publications found

Genes affected

ENSG00000298289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754457.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298289	ENST00000754457.1		n.948C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000266905	ENST00000754342.1		n.*130G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16339 AN: 151992 Hom.: 1969 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0720

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.00255

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0251

Gnomad OTH AF: 0.0951

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

GnomAD4 genome AF: 0.108 AC: 16378 AN: 152110 Hom.: 1979 Cov.: 32 AF XY: 0.106 AC XY: 7853 AN XY: 74366

African (AFR) AF: 0.299 AC: 12397 AN: 41422

American (AMR) AF: 0.0717 AC: 1097 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0720 AC: 250 AN: 3470

East Asian (EAS) AF: 0.0249 AC: 129 AN: 5184

South Asian (SAS) AF: 0.108 AC: 522 AN: 4818

European-Finnish (FIN) AF: 0.00255 AC: 27 AN: 10598

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0251 AC: 1710 AN: 68008

Other (OTH) AF: 0.0998 AC: 211 AN: 2114

Alfa AF: 0.0498 Hom.: 762

Bravo AF: 0.121

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.0
DANN	Benign	0.52
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs2337146; hg19: chr18-46482907;