rs3815018

Variant names:

• chr19-35523716-A-G
• rs3815018
• NM_001166034.2:c.1750-183T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001166034.2(SBSN):​c.1750-183T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,132 control chromosomes in the GnomAD database, including 2,081 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 0.14 (2081 hom., cov: 32)
• Consequence: SBSN NM_001166034.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827
• Publications: 3 publications found

Genes affected

SBSN (HGNC:24950): (suprabasin) Located in extracellular exosome. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.418 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001166034.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBSN	NM_001166034.2	MANE Select	c.1750-183T>C		intron	N/A	NP_001159506.1	Q6UWP8-1
	SBSN	NM_198538.4		c.721-183T>C		intron	N/A	NP_940940.1	Q6UWP8-2
	SBSN	NM_001166035.2		c.487-183T>C		intron	N/A	NP_001159507.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SBSN	ENST00000452271.7	TSL:1 MANE Select	c.1750-183T>C		intron	N/A	ENSP00000430242.1	Q6UWP8-1
	SBSN	ENST00000518157.1	TSL:1	c.721-183T>C		intron	N/A	ENSP00000428771.1	Q6UWP8-2
	SBSN	ENST00000588674.5	TSL:2	c.427-183T>C		intron	N/A	ENSP00000468646.2	K7ESC4

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21779 AN: 152014 Hom.: 2065 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.143 AC: 21831 AN: 152132 Hom.: 2081 Cov.: 32 AF XY: 0.149 AC XY: 11102 AN XY: 74368

African (AFR) AF: 0.151 AC: 6252 AN: 41490

American (AMR) AF: 0.248 AC: 3792 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 403 AN: 3468

East Asian (EAS) AF: 0.433 AC: 2230 AN: 5156

South Asian (SAS) AF: 0.227 AC: 1095 AN: 4824

European-Finnish (FIN) AF: 0.139 AC: 1470 AN: 10592

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0918 AC: 6240 AN: 67990

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.119 Hom.: 1269

Bravo AF: 0.155

Asia WGS AF: 0.337 AC: 1171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.57
PhyloP100		-0.83
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: rs3815018; hg19: chr19-36014618;