rs10489656

Variant names:

• chr1-34765777-A-G
• rs10489656
• ENST00000426886.1:n.208-47368T>C

Variant summary

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

The ENST00000426886.1(SMIM12):​n.208-47368T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,058 control chromosomes in the GnomAD database, including 9,456 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 0.35 (9456 hom., cov: 32)
• Consequence: SMIM12 ENST00000426886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0590
• Publications: 2 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]

ENSG00000255811 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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.208-47368T>C		intron	N/A	ENSP00000429902.1	E5RH51
	ENSG00000255811	ENST00000542839.1	TSL:5	n.111-3902T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52841 AN: 151940 Hom.: 9431 Cov.: 32

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.348 AC: 52915 AN: 152058 Hom.: 9456 Cov.: 32 AF XY: 0.345 AC XY: 25635 AN XY: 74328

African (AFR) AF: 0.386 AC: 16025 AN: 41462

American (AMR) AF: 0.265 AC: 4052 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.356 AC: 1236 AN: 3468

East Asian (EAS) AF: 0.137 AC: 711 AN: 5178

South Asian (SAS) AF: 0.361 AC: 1741 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3930 AN: 10552

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23911 AN: 67966

Other (OTH) AF: 0.345 AC: 728 AN: 2108

Alfa AF: 0.343 Hom.: 14426

Bravo AF: 0.341

Asia WGS AF: 0.255 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.4
DANN	Benign	0.45
PhyloP100		-0.059

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: rs10489656;

hg19: chr1-35231378;

COSMIC: COSV59768812;