rs1481847

Positions:

• chr8-71869260-G-A
• chr8-71869260-G-C
• chr8-71869260-G-T

Variant summary

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

The NR_033652.1(MSC-AS1):​n.776+24838G>A 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 0.557 in 151,942 control chromosomes in the GnomAD database, including 23,681 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 0.56 (23681 hom., cov: 32)
• Consequence: MSC-AS1 NR_033652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584

Genes affected

MSC-AS1 (HGNC:48724): (MSC antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.572 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSC-AS1	NR_033652.1	n.776+24838G>A		intron_variant, non_coding_transcript_variant
MSC-AS1	NR_033651.1	n.307+24838G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSC-AS1	ENST00000518916.5	n.265+24838G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84620 AN: 151824 Hom.: 23654 Cov.: 32

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.516

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.557 AC: 84689 AN: 151942 Hom.: 23681 Cov.: 32 AF XY: 0.555 AC XY: 41221 AN XY: 74254

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.507

Gnomad4 FIN AF: 0.583

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.556

Alfa AF: 0.541 Hom.: 9167

Bravo AF: 0.555

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1481847; hg19: chr8-72781495;