15-78596440-ATT-ATTTTTTT

Position:

• chr15-78596440-ATT-ATTTTTTT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_000743.5(CHRNA3):​c.*163_*164insAAAAA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 0)
• Consequence: CHRNA3 NM_000743.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998

Genes affected

CHRNA3 (HGNC:1957): (cholinergic receptor nicotinic alpha 3 subunit) This locus encodes a member of the nicotinic acetylcholine receptor family of proteins. Members of this family of proteins form pentameric complexes comprised of both alpha and beta subunits. This locus encodes an alpha-type subunit, as it contains characteristic adjacent cysteine residues. The encoded protein is a ligand-gated ion channel that likely plays a role in neurotransmission. Polymorphisms in this gene have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. Alternatively spliced transcript variants have been described. [provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRNA3	NM_000743.5	c.*163_*164insAAAAA		3_prime_UTR_variant	6/6	ENST00000326828.6
CHRNA3	XM_006720382.4	c.*163_*164insAAAAA		3_prime_UTR_variant	6/6
CHRNA3	NM_001166694.2	c.1390-3250_1390-3249insAAAAA		intron_variant
CHRNA3	NR_046313.2	n.1784+99_1784+100insAAAAA		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRNA3	ENST00000326828.6	c.*163_*164insAAAAA		3_prime_UTR_variant	6/6	1	NM_000743.5	P1
CHRNA3	ENST00000348639.7	c.1390-3250_1390-3249insAAAAA		intron_variant		1
CHRNA3	ENST00000559002.5	n.193+99_193+100insAAAAA		intron_variant, non_coding_transcript_variant		1
CHRNA3	ENST00000559658.5	c.*64+99_*64+100insAAAAA		intron_variant, NMD_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Not reported in ClinVar

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: rs71148543; hg19: chr15-78888782;