rs12153391

Variant names:

• chr5-171776434-C-A
• rs12153391
• XM_011534623.2:c.3+2476C>A

Variant summary

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

The XM_011534623.2(SMIM23):​c.3+2476C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,072 control chromosomes in the GnomAD database, including 3,726 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 0.21 (3726 hom., cov: 32)
• Consequence: SMIM23 XM_011534623.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 39 publications found

Genes affected

SMIM23 (HGNC:34440): (small integral membrane protein 23) Predicted to be located in plasma membrane. 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=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31413 AN: 151954 Hom.: 3725 Cov.: 32

Gnomad AFR AF: 0.0954

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.207 AC: 31414 AN: 152072 Hom.: 3726 Cov.: 32 AF XY: 0.210 AC XY: 15643 AN XY: 74332

African (AFR) AF: 0.0950 AC: 3945 AN: 41512

American (AMR) AF: 0.243 AC: 3720 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1051 AN: 3464

East Asian (EAS) AF: 0.398 AC: 2047 AN: 5144

South Asian (SAS) AF: 0.141 AC: 677 AN: 4814

European-Finnish (FIN) AF: 0.284 AC: 2996 AN: 10544

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16308 AN: 67992

Other (OTH) AF: 0.218 AC: 460 AN: 2114

Alfa AF: 0.230 Hom.: 8967

Bravo AF: 0.203

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.7
DANN	Benign	0.80
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs12153391; hg19: chr5-171203438;