8-74350205-T-TA

Position:

• chr8-74350205-T-TA

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The ENST00000675944.1(GDAP1):​c.-237dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.49 (17707 hom., cov: 0)
• Consequence: GDAP1 ENST00000675944.1 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.410

Genes affected

GDAP1 (HGNC:15968): (ganglioside induced differentiation associated protein 1) This gene encodes a member of the ganglioside-induced differentiation-associated protein family, which may play a role in a signal transduction pathway during neuronal development. Mutations in this gene have been associated with various forms of Charcot-Marie-Tooth Disease and neuropathy. Two transcript variants encoding different isoforms and a noncoding variant have been identified for this gene. [provided by RefSeq, Feb 2012]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 8-74350205-T-TA is Benign according to our data. Variant chr8-74350205-T-TA is described in ClinVar as [Benign]. Clinvar id is 1263644.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 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
GDAP1	ENST00000674806.1	c.-215dup		5_prime_UTR_variant	1/6
GDAP1	ENST00000675944.1	c.-237dup		5_prime_UTR_variant	1/6
GDAP1	ENST00000674612.1	c.-17-9921dup		intron_variant

Frequencies

GnomAD3 genomes AF: 0.491 AC: 72117 AN: 146758 Hom.: 17699 Cov.: 0

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.491 AC: 72136 AN: 146790 Hom.: 17707 Cov.: 0 AF XY: 0.492 AC XY: 35101 AN XY: 71320

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.593

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.484

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.517

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 14, 2019

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112601241; hg19: chr8-75262440;