rs11130180

chr3-4914050-A-Cchr3-4914050-A-Gchr3-4914050-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_125916.1(BHLHE40-AS1):n.168-13353T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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: not found (cov: 33)
• Consequence: BHLHE40-AS1 NR_125916.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BHLHE40-AS1	NR_125916.1	n.168-13353T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	NR_037903.3	n.168-13353T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	NR_125915.1	n.308-13353T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BHLHE40-AS1	ENST00000441386.3	n.437-13353T>G		intron_variant, non_coding_transcript_variant		1
BHLHE40-AS1	ENST00000668962.1	n.809-13353T>G		intron_variant, non_coding_transcript_variant
BHLHE40-AS1	ENST00000615178.4	n.168-13353T>G		intron_variant, non_coding_transcript_variant		4
BHLHE40-AS1	ENST00000620618.4	n.308-13353T>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	10
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11130180; hg19: chr3-4955735;