X-154831137-G-T

Variant names:

• chrX-154831137-G-T
• rs5945250
• NM_001162936.4:c.-99-182C>A

Variant summary

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

The NM_001162936.4(SMIM9):​c.-99-182C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 110,130 control chromosomes in the GnomAD database, including 8,177 homozygotes. There are 12,239 hemizygotes in GnomAD. 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 0.39 (8177 hom., 12239 hem., cov: 22)
• Consequence: SMIM9 NM_001162936.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596
• Publications: 7 publications found

Genes affected

SMIM9 (HGNC:41915): (small integral membrane protein 9) Predicted to be located in plasma membrane. 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM9	NM_001162936.4	c.-99-182C>A		intron_variant	Intron 2 of 4	ENST00000369529.2	NP_001156408.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM9	ENST00000369529.2	c.-99-182C>A		intron_variant	Intron 2 of 4	5	NM_001162936.4	ENSP00000358542.1
SMIM9	ENST00000478043.1	n.211-182C>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 43361 AN: 110079 Hom.: 8170 Cov.: 22

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.292

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.394 AC: 43409 AN: 110130 Hom.: 8177 Cov.: 22 AF XY: 0.378 AC XY: 12239 AN XY: 32388

African (AFR) AF: 0.742 AC: 22387 AN: 30185

American (AMR) AF: 0.364 AC: 3767 AN: 10349

Ashkenazi Jewish (ASJ) AF: 0.292 AC: 767 AN: 2631

East Asian (EAS) AF: 0.205 AC: 715 AN: 3493

South Asian (SAS) AF: 0.394 AC: 1017 AN: 2579

European-Finnish (FIN) AF: 0.191 AC: 1107 AN: 5791

Middle Eastern (MID) AF: 0.256 AC: 54 AN: 211

European-Non Finnish (NFE) AF: 0.244 AC: 12877 AN: 52729

Other (OTH) AF: 0.360 AC: 539 AN: 1496

Alfa AF: 0.271 Hom.: 5124

Bravo AF: 0.419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.63
DANN	Benign	0.73
PhyloP100		-0.60
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs5945250; hg19: chrX-154059412;