12-65573407-T-G

Variant names:

• chr12-65573407-T-G
• rs4237904
• ENST00000535315.5:n.293-3359A>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.293-3359A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,032 control chromosomes in the GnomAD database, including 28,868 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 0.58 (28868 hom., cov: 32)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.335-3359A>C		intron_variant	Intron 1 of 3
MSRB3-AS1	NR_120432.1	n.508-3359A>C		intron_variant	Intron 3 of 4
MSRB3-AS1	NR_120433.1	n.434-3359A>C		intron_variant	Intron 2 of 4
MSRB3-AS1	NR_120434.1	n.544-3339A>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000535315.5	n.293-3359A>C		intron_variant	Intron 3 of 4	3
MSRB3-AS1	ENST00000537250.5	n.161-3359A>C		intron_variant	Intron 1 of 3	3
MSRB3-AS1	ENST00000537298.5	n.332-3359A>C		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88106 AN: 151914 Hom.: 28863 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.580 AC: 88111 AN: 152032 Hom.: 28868 Cov.: 32 AF XY: 0.584 AC XY: 43373 AN XY: 74330

African (AFR) AF: 0.264 AC: 10945 AN: 41448

American (AMR) AF: 0.548 AC: 8370 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2618 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2529 AN: 5140

South Asian (SAS) AF: 0.674 AC: 3245 AN: 4814

European-Finnish (FIN) AF: 0.787 AC: 8338 AN: 10588

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.732 AC: 49747 AN: 67974

Other (OTH) AF: 0.640 AC: 1352 AN: 2114

Alfa AF: 0.678 Hom.: 112362

Bravo AF: 0.544

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs4237904; hg19: chr12-65967187;