12-65624693-G-A

Variant names:

• chr12-65624693-G-A
• rs4762106
• ENST00000535315.5:n.193+1919C>T

Variant summary

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

The ENST00000535315.5(MSRB3-AS1):​n.193+1919C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,074 control chromosomes in the GnomAD database, including 34,861 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 0.63 (34861 hom., cov: 32)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 10 publications found

Genes affected

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

ENSG00000256915 (HGNC:):

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 = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.334+17346C>T		intron_variant	Intron 1 of 3
MSRB3-AS1	NR_120432.1	n.408+1919C>T		intron_variant	Intron 2 of 4
MSRB3-AS1	NR_120433.1	n.335-11416C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000535315.5	n.193+1919C>T		intron_variant	Intron 2 of 4	3
MSRB3-AS1	ENST00000537250.5	n.160+17346C>T		intron_variant	Intron 1 of 3	3
MSRB3-AS1	ENST00000537298.5	n.123-11416C>T		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.633 AC: 96129 AN: 151956 Hom.: 34859 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.632 AC: 96131 AN: 152074 Hom.: 34861 Cov.: 32 AF XY: 0.633 AC XY: 47050 AN XY: 74358

African (AFR) AF: 0.274 AC: 11372 AN: 41474

American (AMR) AF: 0.599 AC: 9160 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2796 AN: 3472

East Asian (EAS) AF: 0.440 AC: 2270 AN: 5156

South Asian (SAS) AF: 0.661 AC: 3183 AN: 4814

European-Finnish (FIN) AF: 0.867 AC: 9183 AN: 10592

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.819 AC: 55668 AN: 67968

Other (OTH) AF: 0.694 AC: 1464 AN: 2108

Alfa AF: 0.710 Hom.: 64414

Bravo AF: 0.595

Asia WGS AF: 0.541 AC: 1877 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.82
DANN	Benign	0.25
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs4762106; hg19: chr12-66018473;