rs4129218

Variant names:

• chr12-65564881-G-A
• rs4129218
• ENST00000535315.5:n.350+5110C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-65564881-G-A
• chr12-65564881-G-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.350+5110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,102 control chromosomes in the GnomAD database, including 40,010 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 0.71 (40010 hom., cov: 32)
• Consequence: MSRB3-AS1 ENST00000535315.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659
• Publications: 7 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.392+5110C>T		intron_variant	Intron 2 of 3
MSRB3-AS1	NR_120432.1	n.565+5110C>T		intron_variant	Intron 4 of 4
MSRB3-AS1	NR_120433.1	n.491+5110C>T		intron_variant	Intron 3 of 4
MSRB3-AS1	NR_120434.1	n.621+5110C>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000535315.5	n.350+5110C>T		intron_variant	Intron 4 of 4	3
MSRB3-AS1	ENST00000537250.5	n.218+5110C>T		intron_variant	Intron 2 of 3	3
MSRB3-AS1	ENST00000537298.5	n.389+5110C>T		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107191 AN: 151984 Hom.: 39991 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.858

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.705 AC: 107247 AN: 152102 Hom.: 40010 Cov.: 32 AF XY: 0.708 AC XY: 52609 AN XY: 74352

African (AFR) AF: 0.447 AC: 18513 AN: 41456

American (AMR) AF: 0.671 AC: 10258 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2805 AN: 3470

East Asian (EAS) AF: 0.827 AC: 4270 AN: 5164

South Asian (SAS) AF: 0.776 AC: 3740 AN: 4818

European-Finnish (FIN) AF: 0.858 AC: 9096 AN: 10604

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55877 AN: 68006

Other (OTH) AF: 0.765 AC: 1612 AN: 2106

Alfa AF: 0.713 Hom.: 2728

Bravo AF: 0.678

Asia WGS AF: 0.740 AC: 2572 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.042
DANN	Benign	0.57
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs4129218; hg19: chr12-65958661;