rs776195

Variant names:

• chr12-27435893-A-G
• rs776195
• ENST00000500498.2:n.129+10604T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-27435893-A-G
• chr12-27435893-A-T

Variant summary

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

The ENST00000500498.2(BMAL2-AS1):​n.129+10604T>C variant causes a intron 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 ENST00000500498.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.544
• Publications: 3 publications found

Genes affected

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

SMCO2 (HGNC:34448): (single-pass membrane protein with coiled-coil domains 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000500498.2. 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
	BMAL2-AS1	NR_109975.1		n.138+10604T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMAL2-AS1	ENST00000500498.2	TSL:1	n.129+10604T>C		intron	N/A
	BMAL2-AS1	ENST00000755732.1		n.126-9738T>C		intron	N/A

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

African (AFR) AF: 0.660 AC: 27353 AN: 41456

American (AMR) AF: 0.751 AC: 11487 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.834 AC: 2890 AN: 3466

East Asian (EAS) AF: 0.523 AC: 2703 AN: 5166

South Asian (SAS) AF: 0.670 AC: 3230 AN: 4820

European-Finnish (FIN) AF: 0.682 AC: 7203 AN: 10564

Middle Eastern (MID) AF: 0.884 AC: 260 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51145 AN: 67982

Other (OTH) AF: 0.740 AC: 1562 AN: 2112

Alfa AF: 0.743 Hom.: 114380

Bravo AF: 0.717

Asia WGS AF: 0.570 AC: 1983 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs776195;

hg19: chr12-27588826;