12-65520180-A-G

Variant names:

• chr12-65520180-A-G
• rs1472259
• ENST00000535315.5:n.351-20096T>C

Variant summary

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

The ENST00000535315.5(MSRB3-AS1):​n.351-20096T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 152,006 control chromosomes in the GnomAD database, including 13,433 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 0.42 (13433 hom., cov: 32)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358
• Publications: 5 publications found

Genes affected

MSRB3-AS1 (HGNC:53386): (MSRB3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000535315.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRB3-AS1	NR_120431.1		n.393-20096T>C		intron	N/A
	MSRB3-AS1	NR_120432.1		n.566-20096T>C		intron	N/A
	MSRB3-AS1	NR_120433.1		n.569+18504T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSRB3-AS1	ENST00000535315.5	TSL:3	n.351-20096T>C		intron	N/A
	MSRB3-AS1	ENST00000537250.5	TSL:3	n.219-20096T>C		intron	N/A
	MSRB3-AS1	ENST00000539653.5	TSL:3	n.559+18504T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63265 AN: 151888 Hom.: 13413 Cov.: 32

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.417 AC: 63318 AN: 152006 Hom.: 13433 Cov.: 32 AF XY: 0.416 AC XY: 30941 AN XY: 74292

African (AFR) AF: 0.494 AC: 20474 AN: 41414

American (AMR) AF: 0.301 AC: 4599 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1567 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2191 AN: 5176

South Asian (SAS) AF: 0.399 AC: 1922 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3858 AN: 10560

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27250 AN: 67962

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.401 Hom.: 15360

Bravo AF: 0.416

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.24
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1472259; hg19: chr12-65913960;