rs5996092

Positions:

• chr22-41948404-A-G

Variant summary

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

The NR_172941.1(SMIM45):​n.358+1098A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 151,976 control chromosomes in the GnomAD database, including 28,151 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 0.57 (28151 hom., cov: 31)
• Consequence: SMIM45 NR_172941.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

SMIM45 (HGNC:27930): (small integral membrane protein 45) 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SMIM45	NR_172941.1	n.358+1098A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SMIM45	ENST00000711329.1	c.-15+1098A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86766 AN: 151856 Hom.: 28081 Cov.: 31

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.572 AC: 86893 AN: 151976 Hom.: 28151 Cov.: 31 AF XY: 0.565 AC XY: 41979 AN XY: 74284

Gnomad4 AFR AF: 0.867

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.391

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.532

Alfa AF: 0.493 Hom.: 6006

Bravo AF: 0.604

Asia WGS AF: 0.369 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.98
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5996092; hg19: chr22-42344408;