rs7526035

Variant names:

• chr1-34823438-G-A
• rs7526035
• ENST00000426886.1:n.207+32333C>T

Variant summary

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

The ENST00000426886.1(SMIM12):​n.207+32333C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 151,972 control chromosomes in the GnomAD database, including 23,976 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 0.56 (23976 hom., cov: 32)
• Consequence: SMIM12 ENST00000426886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 6 publications found

Genes affected

SMIM12 (HGNC:25154): (small integral membrane protein 12) 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000426886.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM12	ENST00000426886.1	TSL:1	n.207+32333C>T		intron	N/A	ENSP00000429902.1	E5RH51

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84688 AN: 151854 Hom.: 23948 Cov.: 32

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.558 AC: 84769 AN: 151972 Hom.: 23976 Cov.: 32 AF XY: 0.564 AC XY: 41880 AN XY: 74282

African (AFR) AF: 0.555 AC: 23001 AN: 41438

American (AMR) AF: 0.684 AC: 10447 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3024 AN: 5172

South Asian (SAS) AF: 0.621 AC: 2998 AN: 4826

European-Finnish (FIN) AF: 0.535 AC: 5641 AN: 10546

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.528 AC: 35843 AN: 67940

Other (OTH) AF: 0.548 AC: 1157 AN: 2110

Alfa AF: 0.539 Hom.: 60894

Bravo AF: 0.568

Asia WGS AF: 0.619 AC: 2150 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.68
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7526035;

hg19: chr1-35289039;