8-71869260-G-A

Variant names:

• chr8-71869260-G-A
• rs1481847
• ENST00000457356.9:n.384+24838G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000457356.9(MSC-AS1):​n.384+24838G>A variant causes a intron 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 ENST00000457356.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457356.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSC-AS1	NR_033651.1		n.307+24838G>A		intron	N/A
	MSC-AS1	NR_033652.1		n.776+24838G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSC-AS1	ENST00000457356.9	TSL:1	n.384+24838G>A		intron	N/A
	MSC-AS1	ENST00000518916.5	TSL:3	n.265+24838G>A		intron	N/A
	MSC-AS1	ENST00000519751.6	TSL:4	n.279+24838G>A		intron	N/A

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

African (AFR) AF: 0.554 AC: 22937 AN: 41428

American (AMR) AF: 0.516 AC: 7872 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2162 AN: 3470

East Asian (EAS) AF: 0.589 AC: 3044 AN: 5168

South Asian (SAS) AF: 0.507 AC: 2443 AN: 4814

European-Finnish (FIN) AF: 0.583 AC: 6130 AN: 10518

Middle Eastern (MID) AF: 0.678 AC: 198 AN: 292

European-Non Finnish (NFE) AF: 0.564 AC: 38357 AN: 67972

Other (OTH) AF: 0.556 AC: 1172 AN: 2108

Alfa AF: 0.543 Hom.: 10402

Bravo AF: 0.555

Asia WGS AF: 0.613 AC: 2134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.49
PhyloP100		-0.58
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1481847; hg19: chr8-72781495;