chr12-27435893-A-G

Position:

• chr12-27435893-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109975.1(BMAL2-AS1):​n.138+10604T>C 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 0.714 in 152,054 control chromosomes in the GnomAD database, including 39,065 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 0.71 (39065 hom., cov: 32)
• Consequence: BMAL2-AS1 NR_109975.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544

Genes affected

BMAL2-AS1 (HGNC:49892): (BMAL2 antisense RNA 1)

SMCO2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMAL2-AS1	NR_109975.1	n.138+10604T>C		intron_variant, non_coding_transcript_variant
SMCO2	XM_047428775.1	c.-11+9576A>G		intron_variant			XP_047284731.1
SMCO2	XM_047428776.1	c.51+9576A>G		intron_variant			XP_047284732.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BMAL2-AS1	ENST00000500498.2	n.129+10604T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108502 AN: 151936 Hom.: 39032 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.682

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.714 AC: 108598 AN: 152054 Hom.: 39065 Cov.: 32 AF XY: 0.710 AC XY: 52784 AN XY: 74324

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.751

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.682

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.740

Alfa AF: 0.749 Hom.: 68298

Bravo AF: 0.717

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs776195; hg19: chr12-27588826;