rs9298190

chr8-71932099-T-C

Variant summary

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

The NR_033652.1(MSC-AS1):n.777-30824T>C 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 0.364 in 151,856 control chromosomes in the GnomAD database, including 10,192 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 0.36 (10192 hom., cov: 32)
• Consequence: MSC-AS1 NR_033652.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSC-AS1	NR_033652.1	n.777-30824T>C		intron_variant, non_coding_transcript_variant
MSC-AS1	NR_033651.1	n.308-30824T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSC-AS1	ENST00000518916.5	n.266-30824T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55273 AN: 151738 Hom.: 10181 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.364 AC: 55318 AN: 151856 Hom.: 10192 Cov.: 32 AF XY: 0.366 AC XY: 27155 AN XY: 74234

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.332

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.371

Alfa AF: 0.349 Hom.: 4532

Bravo AF: 0.359

Asia WGS AF: 0.399 AC: 1386 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9298190; hg19: chr8-72844334;