rs5756564

Positions:

• chr22-37216063-T-C
• chr22-37216063-T-G

Variant summary

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

The XM_017028924.2(SSTR3):​c.-612A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,114 control chromosomes in the GnomAD database, including 7,799 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 0.30 (7799 hom., cov: 32)
• Consequence: SSTR3 XM_017028924.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.463

Genes affected

SSTR3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SSTR3	XM_017028924.2	c.-612A>G		5_prime_UTR_variant	1/3		XP_016884413.1
SSTR3	XM_005261721.5	c.-37+4344A>G		intron_variant			XP_005261778.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45719 AN: 151994 Hom.: 7804 Cov.: 32

Gnomad AFR AF: 0.180

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.0996

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.300 AC: 45705 AN: 152114 Hom.: 7799 Cov.: 32 AF XY: 0.291 AC XY: 21676 AN XY: 74364

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.0992

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.309

Alfa AF: 0.199 Hom.: 421

Bravo AF: 0.290

Asia WGS AF: 0.153 AC: 530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5756564; hg19: chr22-37612103;