16-11671758-G-A

Variant names:

• chr16-11671758-G-A
• rs8191288
• NM_003498.6:c.-86+3218G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003498.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNN	NM_003498.6	MANE Select	c.-86+3218G>A		intron	N/A	NP_003489.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SNN	ENST00000329565.6	TSL:1 MANE Select	c.-86+3218G>A		intron	N/A	ENSP00000329287.5

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

African (AFR) AF: 0.508 AC: 21063 AN: 41428

American (AMR) AF: 0.405 AC: 6192 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3470

East Asian (EAS) AF: 0.422 AC: 2173 AN: 5152

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4824

European-Finnish (FIN) AF: 0.526 AC: 5555 AN: 10556

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.556 AC: 37743 AN: 67912

Other (OTH) AF: 0.534 AC: 1123 AN: 2104

Alfa AF: 0.533 Hom.: 10108

Bravo AF: 0.511

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.81
DANN	Benign	0.36
PhyloP100		-0.35
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: rs8191288; hg19: chr16-11765614;