11-118005320-T-C

Variant names:

• chr11-118005320-T-C
• rs11216666
• NM_001394165.1:c.*1090A>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.*1090A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 152,060 control chromosomes in the GnomAD database, including 9,891 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 0.31 (9891 hom., cov: 32)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: SMIM35 NM_001394165.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 11 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 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.*1090A>G		3_prime_UTR	Exon 5 of 5	NP_001381094.1
	SMIM35	NM_001394164.1		c.*1090A>G		3_prime_UTR	Exon 6 of 6	NP_001381093.1
	SMIM35	NM_001394166.1		c.*1090A>G		3_prime_UTR	Exon 4 of 4	NP_001381095.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM35	ENST00000689828.1	MANE Select	c.*1090A>G		3_prime_UTR	Exon 5 of 5	ENSP00000509259.1
	SMIM35	ENST00000636151.1	TSL:5	c.*1134A>G		3_prime_UTR	Exon 7 of 7	ENSP00000490666.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46737 AN: 151912 Hom.: 9857 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.231

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.293

GnomAD4 exome AF: 0.200 AC: 6 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 3 AN XY: 18

African (AFR) AF: 0.500 AC: 2 AN: 4

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.500 AC: 1 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 3 AN: 18

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.308 AC: 46819 AN: 152030 Hom.: 9891 Cov.: 32 AF XY: 0.308 AC XY: 22874 AN XY: 74304

African (AFR) AF: 0.596 AC: 24681 AN: 41442

American (AMR) AF: 0.231 AC: 3529 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2108 AN: 5152

South Asian (SAS) AF: 0.231 AC: 1112 AN: 4816

European-Finnish (FIN) AF: 0.189 AC: 1994 AN: 10572

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11565 AN: 67984

Other (OTH) AF: 0.293 AC: 618 AN: 2106

Alfa AF: 0.286 Hom.: 1580

Bravo AF: 0.324

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.38
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs11216666; hg19: chr11-117876035; COSMIC: COSV107188506; COSMIC: COSV107188506;