1-147757495-G-GGGGCATTTGCCAGAGGTACATACCA

Position:

• chr1-147757495-G-GGGGCATTTGCCAGAGGTACATACCA

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_181703.4(GJA5):​c.*642_*666dupTGGTATGTACCTCTGGCAAATGCCC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: GJA5 NM_181703.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

Genes affected

GJA5 (HGNC:4279): (gap junction protein alpha 5) 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. Mutations in this gene may be associated with atrial fibrillation. Alternatively spliced transcript variants encoding the same isoform have been described. [provided by RefSeq, Jul 2008]

ENSG00000274415 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 1-147757495-G-GGGGCATTTGCCAGAGGTACATACCA is Benign according to our data. Variant chr1-147757495-G-GGGGCATTTGCCAGAGGTACATACCA is described in ClinVar as [Likely_benign]. Clinvar id is 292439.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GJA5	NM_181703.4	c.*642_*666dupTGGTATGTACCTCTGGCAAATGCCC		3_prime_UTR_variant	2/2	ENST00000579774.3	NP_859054.1
GJA5	NM_005266.7	c.*642_*666dupTGGTATGTACCTCTGGCAAATGCCC		3_prime_UTR_variant	2/2		NP_005257.2
LOC102723321	XR_922079.4	n.82-20040_82-20016dupGGGCATTTGCCAGAGGTACATACCA		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GJA5	ENST00000579774	c.*642_*666dupTGGTATGTACCTCTGGCAAATGCCC		3_prime_UTR_variant	2/2	1	NM_181703.4	ENSP00000463851.1
GJA5	ENST00000621517	c.*642_*666dupTGGTATGTACCTCTGGCAAATGCCC		3_prime_UTR_variant	2/2	2		ENSP00000484552.1
ENSG00000274415	ENST00000622634.1	n.229_253dupGGGCATTTGCCAGAGGTACATACCA		non_coding_transcript_exon_variant	1/2	5
ENSG00000274415	ENST00000612401.1	n.308+29_308+53dupGGGCATTTGCCAGAGGTACATACCA		intron_variant		5

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Familial atrial fibrillation Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

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: rs11267274; hg19: chr1-147229628;