rs2233407

Variant names:

• chr14-35405317-T-A
• rs2233407

Your query was ambiguous. Multiple possible variants found:

• chr14-35405317-T-A
• chr14-35405317-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 0.0755 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: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0390

ACMG classification

Verdict is Benign. Variant got -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 id 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.

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: 0.0753 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

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0271

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.0255

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.0543

Gnomad4 OTH AF: 0.0635

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233407; hg19: chr14-35874523;