8-74350205-T-TAAAA

Position:

• chr8-74350205-T-TAAAA

Variant summary

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

The ENST00000675944.1(GDAP1):​c.-240_-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 0.046 (502 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-TAAAA is Benign according to our data. Variant chr8-74350205-T-TAAAA is described in ClinVar as [Benign]. Clinvar id is 1237203.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 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.-218_-215dup		5_prime_UTR_variant	1/6
GDAP1	ENST00000675944.1	c.-240_-237dup		5_prime_UTR_variant	1/6
GDAP1	ENST00000674612.1	c.-17-9924_-17-9921dup		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6744 AN: 146812 Hom.: 503 Cov.: 0

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0218

Gnomad ASJ AF: 0.00289

Gnomad EAS AF: 0.00355

Gnomad SAS AF: 0.00170

Gnomad FIN AF: 0.00118

Gnomad MID AF: 0.0261

Gnomad NFE AF: 0.00121

Gnomad OTH AF: 0.0369

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

GnomAD4 genome AF: 0.0460 AC: 6748 AN: 146844 Hom.: 502 Cov.: 0 AF XY: 0.0434 AC XY: 3098 AN XY: 71360

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0218

Gnomad4 ASJ AF: 0.00289

Gnomad4 EAS AF: 0.00356

Gnomad4 SAS AF: 0.00171

Gnomad4 FIN AF: 0.00118

Gnomad4 NFE AF: 0.00121

Gnomad4 OTH AF: 0.0365

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

Sep 02, 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;