rs17103265

Variant names:

• chr14-35405502-GA-G
• rs17103265
• ENST00000848851.1:n.810delA

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000848851.1(ENSG00000310289):​n.810delA variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0197 in 152,254 control chromosomes in the GnomAD database, including 121 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.020 (121 hom., cov: 30)
• Consequence: ENSG00000310289 ENST00000848851.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.14
• Publications: 7 publications found

Genes affected

ENSG00000310289 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP6: Variant 14-35405502-GA-G is Benign according to our data. Variant chr14-35405502-GA-G is described in ClinVar as Benign. ClinVar VariationId is 1168279.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 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
ENSG00000310289	ENST00000848851.1	n.810delA		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000310246	ENST00000848537.1	n.241+2118delA		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0197 AC: 2995 AN: 152136 Hom.: 121 Cov.: 30

Gnomad AFR AF: 0.0280

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0716

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.00153

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0197 AC: 2997 AN: 152254 Hom.: 121 Cov.: 30 AF XY: 0.0228 AC XY: 1694 AN XY: 74438

African (AFR) AF: 0.0281 AC: 1167 AN: 41530

American (AMR) AF: 0.0109 AC: 166 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3472

East Asian (EAS) AF: 0.175 AC: 908 AN: 5176

South Asian (SAS) AF: 0.0713 AC: 344 AN: 4828

European-Finnish (FIN) AF: 0.0237 AC: 252 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00153 AC: 104 AN: 68020

Other (OTH) AF: 0.0209 AC: 44 AN: 2110

Alfa AF: 0.00967 Hom.: 5

Bravo AF: 0.0191

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Ectodermal dysplasia and immunodeficiency 2 Benign:1

Dec 09, 2024

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
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs17103265; hg19: chr14-35874708;