14-35405648-T-C

Variant names:

• chr14-35405648-T-C
• rs3138053

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.537

ACMG classification

Verdict is Benign. Variant got -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 id 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.

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

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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.264

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.246

Alfa AF: 0.266 Hom.: 1338

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.3
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3138053; hg19: chr14-35874854;