rs4762106

Positions:

• chr12-65624693-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120431.1(MSRB3-AS1):​n.334+17346C>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 0.632 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 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.334+17346C>T		intron_variant, non_coding_transcript_variant
LOC105369806	XR_945028.3	n.70+2328G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.160+17346C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000662138.1	n.93+2328G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.661

Gnomad4 FIN AF: 0.867

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.694

Alfa AF: 0.774 Hom.: 46985

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4762106; hg19: chr12-66018473;