Variant rs578776 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000743.5(CHRNA3):c.*546C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151952 control chromosomes in the gnomAD Genomes database, including 13846 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 0.40 ( 13846 hom., cov: 32)

Consequence

CHRNA3
NM_000743.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.269

Links

CHRNA3 (HGNC:1957):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
CHRNA3	NM_000743.5 linkuse as main transcript	c.*546C>T	3_prime_UTR_variant	6/6	ENST00000326828.6
CHRNA3	XM_006720382.4 linkuse as main transcript	c.*546C>T	3_prime_UTR_variant	6/6
CHRNA3	NM_001166694.2 linkuse as main transcript	c.1390-2867C>T	intron_variant
CHRNA3	NR_046313.2 linkuse as main transcript	n.1784+482C>T	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRNA3	ENST00000326828.6 linkuse as main transcript	c.*546C>T	3_prime_UTR_variant	6/6	1	NM_000743.5	P1	P32297-2
CHRNA3	ENST00000348639.7 linkuse as main transcript	c.1390-2867C>T	intron_variant		1			P32297-3
CHRNA3	ENST00000559002.5 linkuse as main transcript	n.193+482C>T	intron_variant, non_coding_transcript_variant		1
CHRNA3	ENST00000559658.5 linkuse as main transcript	c.*64+482C>T	intron_variant, NMD_transcript_variant		2			P32297-2

Frequencies

GnomAD3 genomes

AF:

0.399

AC:

60651

AN:

151952

Hom.:

13846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.267

Gnomad EAS

AF:

0.785

Gnomad SAS

AF:

0.470

Gnomad FIN

AF:

0.321

Gnomad MID

AF:

0.380

Gnomad NFE

AF:

0.274

Gnomad OTH

AF:

0.386

GnomAD4 exome

AF:

0.293

AC:

242706

AN:

828482

Hom.:

37529

AF XY:

0.292

AC XY:

111870

AN XY:

382700

show subpopulations

Gnomad4 AFR exome

AF:

0.564

Gnomad4 AMR exome

AF:

0.592

Gnomad4 ASJ exome

AF:

0.257

Gnomad4 EAS exome

AF:

0.797

Gnomad4 SAS exome

AF:

0.453

Gnomad4 FIN exome

AF:

0.344

Gnomad4 NFE exome

AF:

0.279

Gnomad4 OTH exome

AF:

0.343

Alfa

AF:

0.306

Hom.:

17525

Bravo

AF:

0.422

Asia WGS

AF:

0.622

AC:

2161

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

Cadd

Benign

0.62

Dann

Benign

0.53

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over