17-44804300-TAAAAAA-TAAAAAAA

Variant names:

• chr17-44804300-T-TA
• rs199789186
• NM_005497.4:c.*326dupT

Variant summary

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

The NM_005497.4(GJC1):​c.*326dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 187,674 control chromosomes in the GnomAD database, including 1,519 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.14 (1494 hom., cov: 29)
  • Exomes 𝑓: 0.14 (25 hom.)
• Consequence: GJC1 NM_005497.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.963

Genes affected

GJC1 (HGNC:4280): (gap junction protein gamma 1) This gene is a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Alternatively spliced transcript variants encoding the same isoform have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 17-44804300-T-TA is Benign according to our data. Variant chr17-44804300-T-TA is described in ClinVar as [Benign]. Clinvar id is 1239515.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJC1	NM_005497.4	c.*326dupT		3_prime_UTR_variant	Exon 3 of 3	ENST00000592524.6	NP_005488.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJC1	ENST00000592524	c.*326dupT		3_prime_UTR_variant	Exon 3 of 3	2	NM_005497.4	ENSP00000467201.1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 20762 AN: 144256 Hom.: 1489 Cov.: 29

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.0991

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.0994

Gnomad MID AF: 0.0714

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.126

GnomAD4 exome AF: 0.137 AC: 5947 AN: 43356 Hom.: 25 Cov.: 0 AF XY: 0.137 AC XY: 3008 AN XY: 21900

Gnomad4 AFR exome AF: 0.182

Gnomad4 AMR exome AF: 0.119

Gnomad4 ASJ exome AF: 0.176

Gnomad4 EAS exome AF: 0.144

Gnomad4 SAS exome AF: 0.128

Gnomad4 FIN exome AF: 0.114

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.140

GnomAD4 genome AF: 0.144 AC: 20778 AN: 144318 Hom.: 1494 Cov.: 29 AF XY: 0.141 AC XY: 9895 AN XY: 69980

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.0996

Gnomad4 ASJ AF: 0.181

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.0994

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.125

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs199789186; hg19: chr17-42881668;