3-4972191-T-C

Variant names:

• chr3-4972191-T-C
• rs6442925
• ENST00000441386.4:n.620+7604A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000441386.4(BHLHE40-AS1):​n.620+7604A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 151,998 control chromosomes in the GnomAD database, including 50,641 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 0.81 (50641 hom., cov: 32)
• Consequence: BHLHE40-AS1 ENST00000441386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.723
• Publications: 18 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000441386.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BHLHE40-AS1	NR_037903.3		n.167+7604A>G		intron	N/A
	BHLHE40-AS1	NR_125915.1		n.167+7604A>G		intron	N/A
	BHLHE40-AS1	NR_125916.1		n.167+7604A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BHLHE40-AS1	ENST00000441386.4	TSL:1	n.620+7604A>G		intron	N/A
	BHLHE40-AS1	ENST00000615178.5	TSL:4	n.174+7604A>G		intron	N/A
	BHLHE40-AS1	ENST00000620618.4	TSL:2	n.167+7604A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 123559 AN: 151880 Hom.: 50597 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.919

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.810

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

GnomAD4 genome AF: 0.814 AC: 123658 AN: 151998 Hom.: 50641 Cov.: 32 AF XY: 0.818 AC XY: 60772 AN XY: 74306

African (AFR) AF: 0.732 AC: 30353 AN: 41446

American (AMR) AF: 0.825 AC: 12612 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2836 AN: 3470

East Asian (EAS) AF: 0.938 AC: 4860 AN: 5180

South Asian (SAS) AF: 0.755 AC: 3642 AN: 4826

European-Finnish (FIN) AF: 0.919 AC: 9648 AN: 10504

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56917 AN: 67972

Other (OTH) AF: 0.813 AC: 1716 AN: 2110

Alfa AF: 0.821 Hom.: 140817

Bravo AF: 0.803

Asia WGS AF: 0.843 AC: 2913 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs6442925; hg19: chr3-5013876;