chr8-72014779-T-A

Variant names:

• chr8-72014779-T-A
• rs1947913
• ENST00000457356.9:n.511-37760T>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.511-37760T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,178 control chromosomes in the GnomAD database, including 5,865 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 0.26 (5865 hom., cov: 33)
• Consequence: MSC-AS1 ENST00000457356.9 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSC-AS1	NR_033651.1	n.434-37760T>A		intron_variant	Intron 2 of 2
MSC-AS1	NR_033652.1	n.1029-37760T>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.511-37760T>A		intron_variant	Intron 2 of 2	1
MSC-AS1	ENST00000518916.5	n.392-37760T>A		intron_variant	Intron 2 of 6	3
MSC-AS1	ENST00000519068.3	n.253-37760T>A		intron_variant	Intron 2 of 5	3

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39824 AN: 152062 Hom.: 5858 Cov.: 33

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.359

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.262 AC: 39863 AN: 152178 Hom.: 5865 Cov.: 33 AF XY: 0.260 AC XY: 19337 AN XY: 74404

African (AFR) AF: 0.383 AC: 15910 AN: 41488

American (AMR) AF: 0.195 AC: 2977 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 888 AN: 3470

East Asian (EAS) AF: 0.359 AC: 1857 AN: 5174

South Asian (SAS) AF: 0.290 AC: 1403 AN: 4830

European-Finnish (FIN) AF: 0.157 AC: 1660 AN: 10606

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14395 AN: 68014

Other (OTH) AF: 0.275 AC: 580 AN: 2110

Alfa AF: 0.101 Hom.: 148

Bravo AF: 0.268

Asia WGS AF: 0.290 AC: 1005 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.74
PhyloP100		-0.16
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: rs1947913; hg19: chr8-72927014;