rs4129218

chr12-65564881-G-Achr12-65564881-G-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.392+5110C>T 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 0.705 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 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.659

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=-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/exons	MANE	UniProt
MSRB3-AS1	NR_120431.1	n.392+5110C>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120432.1	n.565+5110C>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120433.1	n.491+5110C>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120434.1	n.621+5110C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.218+5110C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.858

Gnomad4 NFE AF: 0.822

Gnomad4 OTH AF: 0.765

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4129218; hg19: chr12-65958661;