rs1786176

chr11-118034920-G-A

Variant summary

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

The NM_001394165.1(SMIM35):c.8-19111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 151,866 control chromosomes in the GnomAD database, including 779 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 0.087 (779 hom., cov: 31)
• Consequence: SMIM35 NM_001394165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.708

Genes affected

SMIM35 (HGNC:44179): (small integral membrane protein 35) Predicted to be 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMIM35	NM_001394165.1	c.8-19111C>T		intron_variant		ENST00000689828.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM35	ENST00000689828.1	c.8-19111C>T		intron_variant			NM_001394165.1	P1

Frequencies

GnomAD3 genomes AF: 0.0873 AC: 13246 AN: 151748 Hom.: 780 Cov.: 31

Gnomad AFR AF: 0.0200

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0628

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0970

Gnomad OTH AF: 0.0954

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

GnomAD4 genome AF: 0.0872 AC: 13246 AN: 151866 Hom.: 779 Cov.: 31 AF XY: 0.0925 AC XY: 6862 AN XY: 74210

Gnomad4 AFR AF: 0.0199

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0628

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.0970

Gnomad4 OTH AF: 0.0939

Alfa AF: 0.0919 Hom.: 148

Bravo AF: 0.0821

Asia WGS AF: 0.105 AC: 365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.71
Dann	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1786176; hg19: chr11-117905635;