3-4914050-A-G

Variant names:

• chr3-4914050-A-G
• rs11130180
• ENST00000441386.4:n.621-13353T>C

Variant summary

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

The ENST00000441386.4(BHLHE40-AS1):​n.621-13353T>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 ENST00000441386.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BHLHE40-AS1	ENST00000441386.4	n.621-13353T>C		intron_variant	Intron 1 of 2	1
BHLHE40-AS1	ENST00000615178.5	n.175-13353T>C		intron_variant	Intron 1 of 2	4
BHLHE40-AS1	ENST00000620618.4	n.308-13353T>C		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44349 AN: 151814 Hom.: 7007 Cov.: 33

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.: 33 AF XY: 0.298 AC XY: 22146 AN XY: 74234

African (AFR) AF: 0.232 AC: 9636 AN: 41500

American (AMR) AF: 0.339 AC: 5188 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3468

East Asian (EAS) AF: 0.633 AC: 3258 AN: 5148

South Asian (SAS) AF: 0.426 AC: 2057 AN: 4824

European-Finnish (FIN) AF: 0.308 AC: 3205 AN: 10408

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19061 AN: 67982

Other (OTH) AF: 0.263 AC: 557 AN: 2114

Alfa AF: 0.300 Hom.: 2416

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	11
DANN	Benign	0.82
PhyloP100		-0.012

Splicing

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

Other links and lift over

dbSNP: rs11130180; hg19: chr3-4955735;