rs2233409

Variant names:

• chr14-35405064-G-A
• rs2233409
• ENST00000848851.1:n.369G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000848851.1(ENSG00000310289):​n.369G>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 0.192 in 151,874 control chromosomes in the GnomAD database, including 3,027 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.19 (3027 hom., cov: 31)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.858
• Publications: 42 publications found

Genes affected

ENSG00000310289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 14-35405064-G-A is Benign according to our data. Variant chr14-35405064-G-A is described in ClinVar as Benign. ClinVar VariationId is 1167988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310289	ENST00000848851.1	n.369G>A		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000310246	ENST00000848537.1	n.241+1677G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29107 AN: 151756 Hom.: 3027 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.192 AC: 29103 AN: 151874 Hom.: 3027 Cov.: 31 AF XY: 0.188 AC XY: 13915 AN XY: 74208

African (AFR) AF: 0.135 AC: 5609 AN: 41438

American (AMR) AF: 0.148 AC: 2258 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.0897 AC: 461 AN: 5140

South Asian (SAS) AF: 0.170 AC: 820 AN: 4812

European-Finnish (FIN) AF: 0.230 AC: 2421 AN: 10532

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16259 AN: 67920

Other (OTH) AF: 0.173 AC: 364 AN: 2104

Alfa AF: 0.205 Hom.: 951

Bravo AF: 0.183

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

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

- -

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 19258923, 23487427, 12944982) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.60
DANN	Benign	0.90
PhyloP100		-0.86
PromoterAI		0.019	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2233409; hg19: chr14-35874270;