rs8191288

chr16-11671758-G-Achr16-11671758-G-T

Variant summary

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

The NM_003498.6(SNN):c.-86+3218G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,926 control chromosomes in the GnomAD database, including 21,097 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 0.52 (21097 hom., cov: 32)
• Consequence: SNN NM_003498.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

Genes affected

SNN (HGNC:11149): (stannin) Enables metal ion binding activity. Predicted to be involved in response to toxic substance. Located in cytoplasm. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SNN	NM_003498.6	c.-86+3218G>A		intron_variant		ENST00000329565.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SNN	ENST00000329565.6	c.-86+3218G>A		intron_variant		1	NM_003498.6	P1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79436 AN: 151808 Hom.: 21080 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.523 AC: 79492 AN: 151926 Hom.: 21097 Cov.: 32 AF XY: 0.520 AC XY: 38620 AN XY: 74246

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.405

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.534

Alfa AF: 0.530 Hom.: 8760

Bravo AF: 0.511

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.81
Dann	Benign	0.36

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

Publications

LitVar

Other links and lift over

dbSNP: rs8191288; hg19: chr16-11765614;