rs4129000

Variant names:

• chr12-65559754-C-T
• rs4129000
• ENST00000535315.5:n.350+10237G>A

Variant summary

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

The ENST00000535315.5(MSRB3-AS1):​n.350+10237G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.845 in 152,140 control chromosomes in the GnomAD database, including 54,549 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 0.84 (54545 hom., cov: 30)
  • Exomes 𝑓: 1.0 (4 hom.)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 10 publications found

Genes affected

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

ENSG00000255866 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.392+10237G>A		intron_variant	Intron 2 of 3
MSRB3-AS1	NR_120432.1	n.565+10237G>A		intron_variant	Intron 4 of 4
MSRB3-AS1	NR_120433.1	n.491+10237G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000535315.5	n.350+10237G>A		intron_variant	Intron 4 of 4	3
MSRB3-AS1	ENST00000537250.5	n.218+10237G>A		intron_variant	Intron 2 of 3	3
MSRB3-AS1	ENST00000537298.5	n.390-940G>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.845 AC: 128403 AN: 152016 Hom.: 54508 Cov.: 30

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.932

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.956

Gnomad SAS AF: 0.939

Gnomad FIN AF: 0.927

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.878

GnomAD4 exome AF: 1.00 AC: 8 AN: 8 Hom.: 4 Cov.: 0 AF XY: 1.00 AC XY: 8 AN XY: 8

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.845 AC: 128493 AN: 152132 Hom.: 54545 Cov.: 30 AF XY: 0.849 AC XY: 63131 AN XY: 74360

African (AFR) AF: 0.797 AC: 33068 AN: 41480

American (AMR) AF: 0.772 AC: 11798 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.856 AC: 2968 AN: 3466

East Asian (EAS) AF: 0.957 AC: 4932 AN: 5154

South Asian (SAS) AF: 0.939 AC: 4532 AN: 4824

European-Finnish (FIN) AF: 0.927 AC: 9838 AN: 10610

Middle Eastern (MID) AF: 0.959 AC: 280 AN: 292

European-Non Finnish (NFE) AF: 0.859 AC: 58378 AN: 67998

Other (OTH) AF: 0.875 AC: 1849 AN: 2112

Alfa AF: 0.853 Hom.: 21193

Bravo AF: 0.828

Asia WGS AF: 0.908 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.73
DANN	Benign	0.24
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs4129000; hg19: chr12-65953534;