Variant 1-147757495-G-GGGGCATTTGCCAGAGGTACATACCA details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000579774.3(GJA5):c.*666_*667insTGGTATGTACCTCTGGCAAATGCCC 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
ENST00000579774.3 3_prime_UTR

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.00

Variant links:

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]

GJA5 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

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	Effect	#exon/exons	MANE	Protein
GJA5	NM_181703.4 linkuse as main transcript	c.666_667insTGGTATGTACCTCTGGCAAATGCCC	3_prime_UTR_variant	2/2	ENST00000579774.3	NP_859054.1
LOC102723321	XR_922079.4 linkuse as main transcript	n.82-20040_82-20016dup	intron_variant, non_coding_transcript_variant
GJA5	NM_005266.7 linkuse as main transcript	c.666_667insTGGTATGTACCTCTGGCAAATGCCC	3_prime_UTR_variant	2/2		NP_005257.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
GJA5	ENST00000579774.3 linkuse as main transcript	c.666_667insTGGTATGTACCTCTGGCAAATGCCC	3_prime_UTR_variant	2/2	1	NM_181703.4	ENSP00000463851	P1
	ENST00000612401.1 linkuse as main transcript	n.308+29_308+53dup	splice_donor_region_variant, intron_variant, non_coding_transcript_variant		5
GJA5	ENST00000621517.1 linkuse as main transcript	c.666_667insTGGTATGTACCTCTGGCAAATGCCC	3_prime_UTR_variant	2/2	2		ENSP00000484552	P1
	ENST00000622634.1 linkuse as main transcript	n.229_253dup	non_coding_transcript_exon_variant	1/2	5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

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

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over