chr12-65573407-T-G

Position:

• chr12-65573407-T-G

Variant summary

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

The NR_120431.1(MSRB3-AS1):​n.335-3359A>C 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 0.58 in 152,032 control chromosomes in the GnomAD database, including 28,868 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 0.58 (28868 hom., cov: 32)
• Consequence: MSRB3-AS1 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500

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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.335-3359A>C		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120432.1	n.508-3359A>C		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120433.1	n.434-3359A>C		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120434.1	n.544-3339A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.161-3359A>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88106 AN: 151914 Hom.: 28863 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.491

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.732

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.580 AC: 88111 AN: 152032 Hom.: 28868 Cov.: 32 AF XY: 0.584 AC XY: 43373 AN XY: 74330

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.732

Gnomad4 OTH AF: 0.640

Alfa AF: 0.710 Hom.: 77466

Bravo AF: 0.544

Asia WGS AF: 0.568 AC: 1974 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4237904; hg19: chr12-65967187;