chr1-58575384-T-A

Position:

• chr1-58575384-T-A

Variant summary

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

The 1-58575384-T-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,064 control chromosomes in the GnomAD database, including 2,192 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 0.13 (2192 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TACSTD2 NM_002353.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.258

Genes affected

TACSTD2 (HGNC:11530): (tumor associated calcium signal transducer 2) This intronless gene encodes a carcinoma-associated antigen. This antigen is a cell surface receptor that transduces calcium signals. Mutations of this gene have been associated with gelatinous drop-like corneal dystrophy.[provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -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 = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TACSTD2	NM_002353.3			downstream_gene_variant		ENST00000371225.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TACSTD2	ENST00000371225.4			downstream_gene_variant			NM_002353.3	P1

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19945 AN: 151946 Hom.: 2188 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0623

Gnomad ASJ AF: 0.0854

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0466

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0671

Gnomad OTH AF: 0.0985

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.131 AC: 19965 AN: 152064 Hom.: 2192 Cov.: 32 AF XY: 0.128 AC XY: 9527 AN XY: 74366

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.0854

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0466

Gnomad4 NFE AF: 0.0671

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.108 Hom.: 176

Bravo AF: 0.140

Asia WGS AF: 0.111 AC: 386 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	6.8
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2268943; hg19: chr1-59041056;