rs2233409

chr14-35405064-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.192 in 151,874 control chromosomes in the GnomAD database, including 3,027 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.19 (3027 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.858

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 14-35405064-G-A is Benign according to our data. Variant chr14-35405064-G-A is described in ClinVar as [Benign]. Clinvar id is 1167988.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.236 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: 0.192 AC: 29107 AN: 151756 Hom.: 3027 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.175

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.192 AC: 29103 AN: 151874 Hom.: 3027 Cov.: 31 AF XY: 0.188 AC XY: 13915 AN XY: 74208

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.0897

Gnomad4 SAS AF: 0.170

Gnomad4 FIN AF: 0.230

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.173

Alfa AF: 0.195 Hom.: 509

Bravo AF: 0.183

Asia WGS AF: 0.114 AC: 399 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 19, 2024

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

This variant is associated with the following publications: (PMID: 19258923, 23487427, 12944982) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	0.60
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233409; hg19: chr14-35874270;