14-35405648-T-C

Variant names:

• chr14-35405648-T-C
• rs3138053
• ENST00000848851.1:n.953T>C

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.953T>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 0.262 in 152,070 control chromosomes in the GnomAD database, including 5,389 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (5389 hom., cov: 32)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.537
• Publications: 60 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 14-35405648-T-C is Benign according to our data. Variant chr14-35405648-T-C is described in ClinVar as Benign. ClinVar VariationId is 1167990.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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310289	ENST00000848851.1		n.953T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000310246	ENST00000848537.1		n.241+2261T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39805 AN: 151952 Hom.: 5386 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.285

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: 39828 AN: 152070 Hom.: 5389 Cov.: 32 AF XY: 0.256 AC XY: 19027 AN XY: 74336

African (AFR) AF: 0.248 AC: 10275 AN: 41444

American (AMR) AF: 0.231 AC: 3535 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 916 AN: 3468

East Asian (EAS) AF: 0.126 AC: 650 AN: 5174

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4818

European-Finnish (FIN) AF: 0.250 AC: 2647 AN: 10574

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19687 AN: 67992

Other (OTH) AF: 0.246 AC: 519 AN: 2112

Alfa AF: 0.265 Hom.: 2809

Bravo AF: 0.260

Asia WGS AF: 0.193 AC: 674 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	4.3
DANN	Benign	0.59
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs3138053; hg19: chr14-35874854;