ENST00000441386.4:n.621-24129T>G

Variant names:

• chr3-4924826-A-C
• rs79238327
• ENST00000441386.4:n.621-24129T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000441386.4(BHLHE40-AS1):​n.621-24129T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 152,292 control chromosomes in the GnomAD database, including 40 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 0.013 (40 hom., cov: 31)
• Consequence: BHLHE40-AS1 ENST00000441386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0125 (1907/152292) while in subpopulation AFR AF = 0.0421 (1751/41570). AF 95% confidence interval is 0.0405. There are 40 homozygotes in GnomAd4. There are 882 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 40 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BHLHE40-AS1	NR_037903.3	n.168-24129T>G		intron_variant	Intron 1 of 2
BHLHE40-AS1	NR_125915.1	n.308-24129T>G		intron_variant	Intron 2 of 3
BHLHE40-AS1	NR_125916.1	n.168-24129T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BHLHE40-AS1	ENST00000441386.4	n.621-24129T>G		intron_variant	Intron 1 of 2	1
BHLHE40-AS1	ENST00000615178.5	n.175-24129T>G		intron_variant	Intron 1 of 2	4
BHLHE40-AS1	ENST00000620618.4	n.308-24129T>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.0125 AC: 1900 AN: 152174 Hom.: 40 Cov.: 31

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000621

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000397

Gnomad OTH AF: 0.00813

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

GnomAD4 genome AF: 0.0125 AC: 1907 AN: 152292 Hom.: 40 Cov.: 31 AF XY: 0.0118 AC XY: 882 AN XY: 74480

African (AFR) AF: 0.0421 AC: 1751 AN: 41570

American (AMR) AF: 0.00706 AC: 108 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5190

South Asian (SAS) AF: 0.000621 AC: 3 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10608

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000397 AC: 27 AN: 68018

Other (OTH) AF: 0.00805 AC: 17 AN: 2112

Alfa AF: 0.0125 Hom.: 2

Bravo AF: 0.0143

Asia WGS AF: 0.00318 AC: 11 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.44
PhyloP100		0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs79238327; hg19: chr3-4966511;