rs2587562

chr8-72078803-G-A

Variant summary

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

The ENST00000518916.5(MSC-AS1):n.576+2176G>A 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 0.444 in 151,758 control chromosomes in the GnomAD database, including 15,240 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 0.44 (15240 hom., cov: 32)
• Consequence: MSC-AS1 ENST00000518916.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

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

TRPA1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TRPA1	XM_011517624.3	c.23-3341C>T		intron_variant
TRPA1	XM_011517625.3	c.-54+2373C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSC-AS1	ENST00000518916.5	n.576+2176G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67333 AN: 151640 Hom.: 15224 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.444 AC: 67377 AN: 151758 Hom.: 15240 Cov.: 32 AF XY: 0.444 AC XY: 32928 AN XY: 74158

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.463

Alfa AF: 0.447 Hom.: 24687

Bravo AF: 0.432

Asia WGS AF: 0.371 AC: 1287 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.45
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2587562; hg19: chr8-72991038;