rs11216666

Variant names:

• chr11-118005320-T-A
• rs11216666
• NM_001394165.1:c.*1090A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-118005320-T-A
• chr11-118005320-T-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394165.1(SMIM35):​c.*1090A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

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>T		3_prime_UTR	Exon 5 of 5	NP_001381094.1
	SMIM35	NM_001394164.1		c.*1090A>T		3_prime_UTR	Exon 6 of 6	NP_001381093.1
	SMIM35	NM_001394166.1		c.*1090A>T		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>T		3_prime_UTR	Exon 5 of 5	ENSP00000509259.1
	SMIM35	ENST00000636151.1	TSL:5	c.*1134A>T		3_prime_UTR	Exon 7 of 7	ENSP00000490666.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.2
DANN	Benign	0.49
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;