13-26044784-G-A

Variant names:

• chr13-26044784-G-A
• rs1055252
• NM_001007538.2:c.*1729C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001007538.2(SHISA2):​c.*1729C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,130 control chromosomes in the GnomAD database, including 3,307 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 0.19 (3307 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: SHISA2 NM_001007538.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 7 publications found

Genes affected

SHISA2 (HGNC:20366): (shisa family member 2) Predicted to be involved in negative regulation of Wnt signaling pathway and negative regulation of fibroblast growth factor receptor signaling pathway. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHISA2	NM_001007538.2	c.*1729C>T		3_prime_UTR_variant	Exon 2 of 2	ENST00000319420.4	NP_001007539.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHISA2	ENST00000319420.4	c.*1729C>T		3_prime_UTR_variant	Exon 2 of 2	1	NM_001007538.2	ENSP00000313079.3

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29327 AN: 152012 Hom.: 3310 Cov.: 33

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.207

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.193 AC: 29330 AN: 152130 Hom.: 3307 Cov.: 33 AF XY: 0.198 AC XY: 14753 AN XY: 74378

African (AFR) AF: 0.0728 AC: 3024 AN: 41528

American (AMR) AF: 0.220 AC: 3370 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 601 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1352 AN: 5186

South Asian (SAS) AF: 0.189 AC: 911 AN: 4826

European-Finnish (FIN) AF: 0.317 AC: 3348 AN: 10572

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16039 AN: 67940

Other (OTH) AF: 0.207 AC: 437 AN: 2114

Alfa AF: 0.226 Hom.: 7558

Bravo AF: 0.184

Asia WGS AF: 0.178 AC: 618 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.50
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1055252; hg19: chr13-26618922;