rs716392

Positions:

• chr17-55512052-G-T

Variant summary

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

The XM_047435094.1(SMIM36):​c.46-691C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 152,020 control chromosomes in the GnomAD database, including 33,432 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 0.65 (33432 hom., cov: 32)
• Consequence: SMIM36 XM_047435094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

SMIM36 (HGNC:53654): (small integral membrane protein 36) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SMIM36	XM_047435094.1	c.46-691C>A		intron_variant			XP_047291050.1
SMIM36	XM_047435095.1	c.46-691C>A		intron_variant			XP_047291051.1
		n.55512052G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99331 AN: 151902 Hom.: 33383 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.703

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.654 AC: 99440 AN: 152020 Hom.: 33432 Cov.: 32 AF XY: 0.660 AC XY: 49034 AN XY: 74292

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.650

Alfa AF: 0.573 Hom.: 26536

Bravo AF: 0.661

Asia WGS AF: 0.787 AC: 2735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.84
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs716392; hg19: chr17-53589413;