rs1472259

chr12-65520180-A-Gchr12-65520180-A-T

Variant summary

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

The NR_120431.1(MSRB3-AS1):n.393-20096T>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 0.417 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 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.358

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSRB3-AS1	NR_120431.1	n.393-20096T>C		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120432.1	n.566-20096T>C		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120433.1	n.569+18504T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.219-20096T>C		intron_variant, non_coding_transcript_variant		3
MSRB3-AS1	ENST00000535315.5	n.351-20096T>C		intron_variant, non_coding_transcript_variant		3
MSRB3-AS1	ENST00000539653.5	n.559+18504T>C		intron_variant, non_coding_transcript_variant		3
MSRB3-AS1	ENST00000540652.5	n.529-20096T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.452

Gnomad4 EAS AF: 0.423

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.417

Alfa AF: 0.400 Hom.: 11570

Bravo AF: 0.416

Asia WGS AF: 0.395 AC: 1371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.5
Dann	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1472259; hg19: chr12-65913960;