rs3138050

Variant names:

• chr14-35406163-G-A
• rs3138050
• ENST00000848537.1:n.241+2776G>A

Your query was ambiguous. Multiple possible variants found:

• chr14-35406163-G-A
• chr14-35406163-G-C
• chr14-35406163-G-T

Variant summary

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

The ENST00000848537.1(ENSG00000310246):​n.241+2776G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 151,542 control chromosomes in the GnomAD database, including 4,193 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 0.23 (4193 hom., cov: 31)
• Consequence: ENSG00000310246 ENST00000848537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 6 publications found

Genes affected

ENSG00000310246 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848537.1. 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
	ENSG00000310246	ENST00000848537.1		n.241+2776G>A		intron	N/A
	ENSG00000310289	ENST00000848851.1		n.*107G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35429 AN: 151424 Hom.: 4184 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.234 AC: 35461 AN: 151542 Hom.: 4193 Cov.: 31 AF XY: 0.234 AC XY: 17328 AN XY: 74066

African (AFR) AF: 0.254 AC: 10483 AN: 41248

American (AMR) AF: 0.235 AC: 3567 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.189 AC: 656 AN: 3462

East Asian (EAS) AF: 0.290 AC: 1491 AN: 5148

South Asian (SAS) AF: 0.259 AC: 1245 AN: 4814

European-Finnish (FIN) AF: 0.239 AC: 2494 AN: 10456

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14832 AN: 67904

Other (OTH) AF: 0.215 AC: 452 AN: 2098

Alfa AF: 0.122 Hom.: 227

Bravo AF: 0.235

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs3138050; hg19: chr14-35875369;