rs13053175

chr22-37217269-C-T

Variant summary

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

The XM_005261721.5(SSTR3):c.-37+3138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 152,118 control chromosomes in the GnomAD database, including 8,910 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 0.33 (8910 hom., cov: 33)
• Consequence: SSTR3 XM_005261721.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

Genes affected

SSTR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSTR3	XM_005261721.5	c.-37+3138G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49813 AN: 151998 Hom.: 8914 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.0895

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.327 AC: 49791 AN: 152118 Hom.: 8910 Cov.: 33 AF XY: 0.316 AC XY: 23507 AN XY: 74360

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.0891

Gnomad4 SAS AF: 0.246

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.421

Gnomad4 OTH AF: 0.336

Alfa AF: 0.391 Hom.: 15783

Bravo AF: 0.321

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.56
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13053175; hg19: chr22-37613309;