rs3138052

Variant names:

• chr14-35405815-T-C
• rs3138052
• ENST00000848851.1:n.1120T>C

Variant summary

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

The ENST00000848851.1(ENSG00000310289):​n.1120T>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 0.261 in 152,022 control chromosomes in the GnomAD database, including 5,349 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 0.26 (5349 hom., cov: 32)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 4 publications found

Genes affected

ENSG00000310289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848851.1. 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
	ENSG00000310289	ENST00000848851.1		n.1120T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000310246	ENST00000848537.1		n.241+2428T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39638 AN: 151904 Hom.: 5346 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.244

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

GnomAD4 genome AF: 0.261 AC: 39661 AN: 152022 Hom.: 5349 Cov.: 32 AF XY: 0.255 AC XY: 18960 AN XY: 74304

African (AFR) AF: 0.247 AC: 10251 AN: 41462

American (AMR) AF: 0.229 AC: 3496 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3464

East Asian (EAS) AF: 0.123 AC: 637 AN: 5164

South Asian (SAS) AF: 0.263 AC: 1270 AN: 4824

European-Finnish (FIN) AF: 0.259 AC: 2737 AN: 10584

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19574 AN: 67938

Other (OTH) AF: 0.241 AC: 507 AN: 2104

Alfa AF: 0.261 Hom.: 785

Bravo AF: 0.258

Asia WGS AF: 0.186 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.1
DANN	Benign	0.29
PhyloP100		0.11

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3138052;

hg19: chr14-35875021;