chr14-35405317-T-A

Variant names:

• chr14-35405317-T-A
• rs2233407
• ENST00000848851.1:n.622T>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.622T>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 0.0755 in 151,970 control chromosomes in the GnomAD database, including 543 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.075 (543 hom., cov: 32)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0390
• Publications: 14 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=-0.76).
• BP6: Variant 14-35405317-T-A is Benign according to our data. Variant chr14-35405317-T-A is described in ClinVar as Benign. ClinVar VariationId is 1165091.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 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.622T>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000310246	ENST00000848537.1		n.241+1930T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0753 AC: 11439 AN: 151854 Hom.: 539 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0552

Gnomad ASJ AF: 0.0271

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.0257

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0543

Gnomad OTH AF: 0.0565

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

GnomAD4 genome AF: 0.0755 AC: 11469 AN: 151970 Hom.: 543 Cov.: 32 AF XY: 0.0776 AC XY: 5763 AN XY: 74272

African (AFR) AF: 0.102 AC: 4230 AN: 41412

American (AMR) AF: 0.0556 AC: 849 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0271 AC: 94 AN: 3472

East Asian (EAS) AF: 0.174 AC: 897 AN: 5152

South Asian (SAS) AF: 0.0255 AC: 123 AN: 4824

European-Finnish (FIN) AF: 0.133 AC: 1407 AN: 10552

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0543 AC: 3691 AN: 67978

Other (OTH) AF: 0.0635 AC: 134 AN: 2110

Alfa AF: 0.0339 Hom.: 29

Bravo AF: 0.0726

Asia WGS AF: 0.111 AC: 383 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:1

Jan 27, 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	-0.76
CADD	Benign	3.9
DANN	Benign	0.61
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs2233407; hg19: chr14-35874523;