14-35405593-G-A

Variant names:

• chr14-35405593-G-A
• rs2233406
• ENST00000848851.1:n.898G>A

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000848851.1(ENSG00000310289):​n.898G>A 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 0.262 in 151,994 control chromosomes in the GnomAD database, including 5,386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (5386 hom., cov: 32)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200
• Publications: 81 publications found

Genes affected

ENSG00000310289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 14-35405593-G-A is Benign according to our data. Variant chr14-35405593-G-A is described in ClinVar as Benign. ClinVar VariationId is 1167989.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310289	ENST00000848851.1		n.898G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000310246	ENST00000848537.1		n.241+2206G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39813 AN: 151876 Hom.: 5385 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.262 AC: 39827 AN: 151994 Hom.: 5386 Cov.: 32 AF XY: 0.256 AC XY: 19039 AN XY: 74278

African (AFR) AF: 0.247 AC: 10219 AN: 41452

American (AMR) AF: 0.230 AC: 3514 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 906 AN: 3462

East Asian (EAS) AF: 0.126 AC: 650 AN: 5178

South Asian (SAS) AF: 0.272 AC: 1311 AN: 4816

European-Finnish (FIN) AF: 0.259 AC: 2734 AN: 10554

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19690 AN: 67942

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.278 Hom.: 8243

Bravo AF: 0.260

Asia WGS AF: 0.191 AC: 669 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.6
DANN	Benign	0.68
PhyloP100		-0.020

Splicing

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

Other links and lift over

dbSNP: rs2233406; hg19: chr14-35874799;