rs11961755

chr6-121445140-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000165.5(GJA1):c.-16-1692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,094 control chromosomes in the GnomAD database, including 4,113 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4113 hom., cov: 32)
• Consequence: GJA1 NM_000165.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

GJA1 (HGNC:4274): (gap junction protein alpha 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. The encoded protein is the major protein of gap junctions in the heart that are thought to have a crucial role in the synchronized contraction of the heart and in embryonic development. A related intronless pseudogene has been mapped to chromosome 5. Mutations in this gene have been associated with oculodentodigital dysplasia, autosomal recessive craniometaphyseal dysplasia and heart malformations. [provided by RefSeq, May 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJA1	NM_000165.5	c.-16-1692G>A		intron_variant		ENST00000282561.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GJA1	ENST00000282561.4	c.-16-1692G>A		intron_variant		1	NM_000165.5	P1
GJA1	ENST00000647564.1	c.-16-1692G>A		intron_variant				P1
GJA1	ENST00000649003.1	c.-16-1692G>A		intron_variant				P1
GJA1	ENST00000650427.1	c.-16-1692G>A		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34321 AN: 151976 Hom.: 4110 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0260

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.238

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

GnomAD4 genome AF: 0.226 AC: 34340 AN: 152094 Hom.: 4113 Cov.: 32 AF XY: 0.227 AC XY: 16892 AN XY: 74356

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.0261

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.234

Alfa AF: 0.254 Hom.: 2469

Bravo AF: 0.212

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.85
Dann	Benign	0.67

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: rs11961755; hg19: chr6-121766286;