chr19-35523716-A-G

Position:

• chr19-35523716-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SBSN	NM_001166034.2	c.1750-183T>C		intron_variant		ENST00000452271.7	NP_001159506.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SBSN	ENST00000452271.7	c.1750-183T>C		intron_variant		1	NM_001166034.2	ENSP00000430242.1
SBSN	ENST00000518157.1	c.721-183T>C		intron_variant		1		ENSP00000428771.1
SBSN	ENST00000588674.5	c.427-183T>C		intron_variant		2		ENSP00000468646.2

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.433

Gnomad4 SAS AF: 0.227

Gnomad4 FIN AF: 0.139

Gnomad4 NFE AF: 0.0918

Gnomad4 OTH AF: 0.138

Alfa AF: 0.119 Hom.: 1082

Bravo AF: 0.155

Asia WGS AF: 0.337 AC: 1171 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

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: rs3815018; hg19: chr19-36014618;