rs2245210

Positions:

• chr12-65537114-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.392+32877C>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 0.173 in 152,140 control chromosomes in the GnomAD database, including 2,706 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 0.17 (2706 hom., cov: 33)
• Consequence: MSRB3-AS1 NR_120431.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSRB3-AS1	NR_120431.1	n.392+32877C>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120432.1	n.565+32877C>T		intron_variant, non_coding_transcript_variant
MSRB3-AS1	NR_120433.1	n.569+1570C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSRB3-AS1	ENST00000537250.5	n.218+32877C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26246 AN: 152022 Hom.: 2701 Cov.: 33

Gnomad AFR AF: 0.0750

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.173 AC: 26258 AN: 152140 Hom.: 2706 Cov.: 33 AF XY: 0.171 AC XY: 12734 AN XY: 74376

Gnomad4 AFR AF: 0.0749

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0963

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.171

Alfa AF: 0.207 Hom.: 3677

Bravo AF: 0.181

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2245210; hg19: chr12-65930894;