rs79238327

chr3-4924826-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_125916.1(BHLHE40-AS1):n.168-24129T>G variant causes a intron, non coding transcript 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 NR_125916.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.313

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 40 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BHLHE40-AS1	NR_125916.1	n.168-24129T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	NR_037903.3	n.168-24129T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	NR_125915.1	n.308-24129T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BHLHE40-AS1	ENST00000441386.3	n.437-24129T>G		intron_variant, non_coding_transcript_variant		1
BHLHE40-AS1	ENST00000668962.1	n.809-24129T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	ENST00000615178.4	n.168-24129T>G		intron_variant, non_coding_transcript_variant		4
BHLHE40-AS1	ENST00000620618.4	n.308-24129T>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0421

Gnomad4 AMR AF: 0.00706

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000621

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000397

Gnomad4 OTH AF: 0.00805

Alfa AF: 0.0105 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs79238327; hg19: chr3-4966511;