NM_001394165.1:c.8-17312A>G

Variant names:

• chr11-118033121-T-C
• rs4936417
• NM_001394165.1:c.8-17312A>G

Variant summary

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

The NM_001394165.1(SMIM35):​c.8-17312A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,168 control chromosomes in the GnomAD database, including 4,717 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 0.23 (4717 hom., cov: 32)
• Consequence: SMIM35 NM_001394165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 4 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=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.309 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	NM_001394165.1	MANE Select	c.8-17312A>G		intron	N/A	NP_001381094.1
	SMIM35	NM_001354434.2		c.123-1152A>G		intron	N/A	NP_001341363.1
	SMIM35	NM_001394164.1		c.-94-1152A>G		intron	N/A	NP_001381093.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	ENST00000689828.1	MANE Select	c.8-17312A>G		intron	N/A	ENSP00000509259.1
	SMIM35	ENST00000527329.5	TSL:1	n.267-17312A>G		intron	N/A
	SMIM35	ENST00000527695.1	TSL:1	n.196-17312A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34943 AN: 152050 Hom.: 4714 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.223

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0603

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.230 AC: 34962 AN: 152168 Hom.: 4717 Cov.: 32 AF XY: 0.223 AC XY: 16559 AN XY: 74372

African (AFR) AF: 0.107 AC: 4464 AN: 41536

American (AMR) AF: 0.237 AC: 3619 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3468

East Asian (EAS) AF: 0.0600 AC: 311 AN: 5180

South Asian (SAS) AF: 0.166 AC: 802 AN: 4826

European-Finnish (FIN) AF: 0.294 AC: 3102 AN: 10568

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.313 AC: 21271 AN: 67990

Other (OTH) AF: 0.222 AC: 467 AN: 2108

Alfa AF: 0.275 Hom.: 20557

Bravo AF: 0.219

Asia WGS AF: 0.111 AC: 386 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.4
DANN	Benign	0.92
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs4936417; hg19: chr11-117903836;