rs7526035

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM12	ENST00000426886.1	n.207+32333C>T		intron_variant	Intron 2 of 4	1		ENSP00000429902.1

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

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.684

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.548

Alfa AF: 0.538 Hom.: 19174

Bravo AF: 0.568

Asia WGS AF: 0.619 AC: 2150 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7526035; hg19: chr1-35289039;