rs8191288

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.350
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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
SNNNM_003498.6 linkuse as main transcriptc.-86+3218G>A intron_variant ENST00000329565.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SNNENST00000329565.6 linkuse as main transcriptc.-86+3218G>A intron_variant 1 NM_003498.6 P1

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs8191288; hg19: chr16-11765614; API