rs2233406

Variant names:

• chr14-35405593-G-A
• rs2233406

Your query was ambiguous. Multiple possible variants found:

• chr14-35405593-G-A
• chr14-35405593-G-C
• chr14-35405593-G-T

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 151,994 control chromosomes in the GnomAD database, including 5,386 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.26 (5386 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0200

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 14-35405593-G-A is Benign according to our data. Variant chr14-35405593-G-A is described in ClinVar as [Benign]. Clinvar id is 1167989.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: 39813 AN: 151876 Hom.: 5385 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.278

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: 39827 AN: 151994 Hom.: 5386 Cov.: 32 AF XY: 0.256 AC XY: 19039 AN XY: 74278

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.245

Alfa AF: 0.280 Hom.: 5828

Bravo AF: 0.260

Asia WGS AF: 0.191 AC: 669 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	2.6
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233406; hg19: chr14-35874799;