11-118034920-G-A

Variant names:

• chr11-118034920-G-A
• rs1786176
• NM_001394165.1:c.8-19111C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394165.1. 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
	SMIM35	NM_001394165.1	MANE Select	c.8-19111C>T		intron	N/A	NP_001381094.1	A0A1B0GVV1
	SMIM35	NM_001354434.2		c.123-2951C>T		intron	N/A	NP_001341363.1
	SMIM35	NM_001394164.1		c.-94-2951C>T		intron	N/A	NP_001381093.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	ENST00000689828.1	MANE Select	c.8-19111C>T		intron	N/A	ENSP00000509259.1	A0A1B0GVV1
	SMIM35	ENST00000527329.5	TSL:1	n.267-19111C>T		intron	N/A
	SMIM35	ENST00000527695.1	TSL:1	n.196-19111C>T		intron	N/A

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

African (AFR) AF: 0.0199 AC: 823 AN: 41422

American (AMR) AF: 0.147 AC: 2242 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0628 AC: 218 AN: 3470

East Asian (EAS) AF: 0.132 AC: 678 AN: 5142

South Asian (SAS) AF: 0.0926 AC: 446 AN: 4816

European-Finnish (FIN) AF: 0.183 AC: 1922 AN: 10510

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0970 AC: 6592 AN: 67956

Other (OTH) AF: 0.0939 AC: 198 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.71
DANN	Benign	0.77
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1786176; hg19: chr11-117905635;