1-34720244-T-C

Position:

• chr1-34720244-T-C

Variant summary

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

The ENST00000426886.1(SMIM12):​c.208-1835A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 152,040 control chromosomes in the GnomAD database, including 17,325 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 0.47 (17325 hom., cov: 32)
• Consequence: SMIM12 ENST00000426886.1 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.45

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]

LOC105378642 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378642	XR_001737971.2	n.109-1835A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SMIM12	ENST00000426886.1	c.208-1835A>G		intron_variant, NMD_transcript_variant		1		ENSP00000429902

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71767 AN: 151922 Hom.: 17322 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.472 AC: 71808 AN: 152040 Hom.: 17325 Cov.: 32 AF XY: 0.470 AC XY: 34918 AN XY: 74290

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.457

Alfa AF: 0.434 Hom.: 24505

Bravo AF: 0.480

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0080
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489658; hg19: chr1-35185845;