rs1481848

Variant names:

• chr8-71869190-A-T
• rs1481848
• ENST00000457356.9:n.384+24768A>T

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+24768A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 151,908 control chromosomes in the GnomAD database, including 28,816 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 0.61 (28816 hom., cov: 31)
• Consequence: MSC-AS1 ENST00000457356.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 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=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSC-AS1	NR_033651.1	n.307+24768A>T		intron_variant	Intron 1 of 2
MSC-AS1	NR_033652.1	n.776+24768A>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSC-AS1	ENST00000457356.9	n.384+24768A>T		intron_variant	Intron 1 of 2	1
MSC-AS1	ENST00000518916.5	n.265+24768A>T		intron_variant	Intron 1 of 6	3
MSC-AS1	ENST00000519751.6	n.279+24768A>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92631 AN: 151790 Hom.: 28770 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.610 AC: 92737 AN: 151908 Hom.: 28816 Cov.: 31 AF XY: 0.607 AC XY: 45067 AN XY: 74226

African (AFR) AF: 0.732 AC: 30327 AN: 41424

American (AMR) AF: 0.541 AC: 8262 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2173 AN: 3468

East Asian (EAS) AF: 0.592 AC: 3055 AN: 5158

South Asian (SAS) AF: 0.518 AC: 2488 AN: 4806

European-Finnish (FIN) AF: 0.582 AC: 6106 AN: 10500

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38488 AN: 67960

Other (OTH) AF: 0.599 AC: 1263 AN: 2110

Alfa AF: 0.593 Hom.: 3354

Bravo AF: 0.615

Asia WGS AF: 0.617 AC: 2144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.62
DANN	Benign	0.48
PhyloP100		-1.3
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: rs1481848; hg19: chr8-72781425;