chr1-34823438-G-A

Position:

• chr1-34823438-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426886.1(SMIM12):​c.207+32333C>T variant causes a intron, NMD transcript 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, NMD_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMIM12	ENST00000426886.1	c.207+32333C>T		intron_variant, NMD_transcript_variant		1		ENSP00000429902

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;