chr15-78596749-TAAAA-T
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_000743.5(CHRNA3):c.1390-21_1390-18del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000464 in 1,584,712 control chromosomes in the GnomAD database, including 5 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0025 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00025 ( 4 hom. )
Consequence
CHRNA3
NM_000743.5 intron
NM_000743.5 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.401
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 15-78596749-TAAAA-T is Benign according to our data. Variant chr15-78596749-TAAAA-T is described in ClinVar as [Benign]. Clinvar id is 1971188.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00251 (381/151996) while in subpopulation AFR AF= 0.00875 (363/41484). AF 95% confidence interval is 0.00801. There are 1 homozygotes in gnomad4. There are 182 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHRNA3 | NM_000743.5 | c.1390-21_1390-18del | intron_variant | ENST00000326828.6 | NP_000734.2 | |||
CHRNA3 | NM_001166694.2 | c.1390-3562_1390-3559del | intron_variant | NP_001160166.1 | ||||
CHRNA3 | XM_006720382.4 | c.1189-21_1189-18del | intron_variant | XP_006720445.1 | ||||
CHRNA3 | NR_046313.2 | n.1592-21_1592-18del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNA3 | ENST00000326828.6 | c.1390-21_1390-18del | intron_variant | 1 | NM_000743.5 | ENSP00000315602 | P1 | |||
CHRNA3 | ENST00000348639.7 | c.1390-3562_1390-3559del | intron_variant | 1 | ENSP00000267951 | |||||
CHRNA3 | ENST00000559658.5 | c.1390-21_1390-18del | intron_variant, NMD_transcript_variant | 2 | ENSP00000452896 | |||||
CHRNA3 | ENST00000559002.5 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00252 AC: 382AN: 151878Hom.: 1 Cov.: 32
GnomAD3 genomes
AF:
AC:
382
AN:
151878
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.000740 AC: 163AN: 220344Hom.: 2 AF XY: 0.000591 AC XY: 71AN XY: 120218
GnomAD3 exomes
AF:
AC:
163
AN:
220344
Hom.:
AF XY:
AC XY:
71
AN XY:
120218
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.000248 AC: 355AN: 1432716Hom.: 4 AF XY: 0.000223 AC XY: 159AN XY: 712588
GnomAD4 exome
AF:
AC:
355
AN:
1432716
Hom.:
AF XY:
AC XY:
159
AN XY:
712588
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.00251 AC: 381AN: 151996Hom.: 1 Cov.: 32 AF XY: 0.00245 AC XY: 182AN XY: 74286
GnomAD4 genome
AF:
AC:
381
AN:
151996
Hom.:
Cov.:
32
AF XY:
AC XY:
182
AN XY:
74286
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 23, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at