rs3138053

chr14-35405648-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2024

- -

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;