rs2233407

chr14-35405317-T-Achr14-35405317-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 02, 2024

- -

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;