Genetic Variant BHLHE40-AS1:n.437-13353T>C (chr3-4914050-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000441386.3(BHLHE40-AS1):n.437-13353T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,932 control chromosomes in the GnomAD database, including 7,011 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 0.29 ( 7011 hom., cov: 33)

Consequence

BHLHE40-AS1
ENST00000441386.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0120

Variant links:

Genes affected

BHLHE40-AS1 (HGNC:44471): (BHLHE40 antisense RNA 1)

BHLHE40-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
BHLHE40-AS1	NR_037903.3 link	n.168-13353T>C	intron_variant	Intron 1 of 2
BHLHE40-AS1	NR_125915.1 link	n.308-13353T>C	intron_variant	Intron 2 of 3
BHLHE40-AS1	NR_125916.1 link	n.168-13353T>C	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
BHLHE40-AS1	ENST00000441386.3 link	n.437-13353T>C	intron_variant	Intron 1 of 2	1
BHLHE40-AS1	ENST00000615178.4 link	n.168-13353T>C	intron_variant	Intron 1 of 2	4
BHLHE40-AS1	ENST00000620618.4 link	n.308-13353T>C	intron_variant	Intron 2 of 3	2
BHLHE40-AS1	ENST00000668962.1 link	n.809-13353T>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.292

AC:

44349

AN:

151814

Hom.:

7007

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.356

Gnomad AMR

AF:

0.339

Gnomad ASJ

AF:

0.291

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.427

Gnomad FIN

AF:

0.308

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.261

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

GnomAD4 genome

AF:

0.292

AC:

44367

AN:

151932

Hom.:

7011

Cov.:

AF XY:

0.298

AC XY:

22146

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.232

Gnomad4 AMR

AF:

0.339

Gnomad4 ASJ

AF:

0.291

Gnomad4 EAS

AF:

0.633

Gnomad4 SAS

AF:

0.426

Gnomad4 FIN

AF:

0.308

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.263

Alfa

AF:

0.281

Hom.:

1012

Bravo

AF:

0.292

Asia WGS

AF:

0.479

AC:

1663

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

DANN

Benign

0.82

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over