chr8-71977832-G-A

Variant names:

• chr8-71977832-G-A
• rs13258140
• ENST00000457356.9:n.510+14784G>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.510+14784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,182 control chromosomes in the GnomAD database, including 1,601 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 0.13 (1601 hom., cov: 32)
• Consequence: MSC-AS1 ENST00000457356.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSC-AS1	NR_033651.1	n.433+14784G>A		intron_variant	Intron 2 of 2
MSC-AS1	NR_033652.1	n.1028+12298G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSC-AS1	ENST00000457356.9	n.510+14784G>A		intron_variant	Intron 2 of 2	1
MSC-AS1	ENST00000518916.5	n.391+14784G>A		intron_variant	Intron 2 of 6	3
MSC-AS1	ENST00000519068.3	n.252+12298G>A		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19651 AN: 152064 Hom.: 1601 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.0865

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0968

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.129 AC: 19670 AN: 152182 Hom.: 1601 Cov.: 32 AF XY: 0.128 AC XY: 9536 AN XY: 74394

African (AFR) AF: 0.223 AC: 9269 AN: 41496

American (AMR) AF: 0.112 AC: 1713 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3468

East Asian (EAS) AF: 0.0315 AC: 163 AN: 5182

South Asian (SAS) AF: 0.0866 AC: 417 AN: 4816

European-Finnish (FIN) AF: 0.0793 AC: 839 AN: 10584

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0969 AC: 6589 AN: 68018

Other (OTH) AF: 0.114 AC: 240 AN: 2114

Alfa AF: 0.109 Hom.: 1425

Bravo AF: 0.133

Asia WGS AF: 0.0610 AC: 214 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		-0.37
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: rs13258140; hg19: chr8-72890067;