rs716392

Variant names:

• chr17-55512052-G-T
• rs716392
• ENST00000799638.1:n.98+10239G>T

Variant summary

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

The ENST00000799638.1(ENSG00000304090):​n.98+10239G>T 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: ENSG00000304090 ENST00000799638.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 3 publications found

Genes affected

ENSG00000304090 (HGNC:):

SMIM36 (HGNC:53654): (small integral membrane protein 36) 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=-0.84).
• 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 rank	MANE	Protein	UniProt
SMIM36	XM_047435094.1	c.46-691C>A		intron_variant	Intron 4 of 4		XP_047291050.1
SMIM36	XM_047435095.1	c.46-691C>A		intron_variant	Intron 3 of 3		XP_047291051.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304090	ENST00000799638.1	n.98+10239G>T		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.801 AC: 33222 AN: 41474

American (AMR) AF: 0.654 AC: 10003 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2300 AN: 3470

East Asian (EAS) AF: 0.768 AC: 3962 AN: 5156

South Asian (SAS) AF: 0.710 AC: 3413 AN: 4808

European-Finnish (FIN) AF: 0.657 AC: 6940 AN: 10564

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37412 AN: 67950

Other (OTH) AF: 0.650 AC: 1370 AN: 2108

Alfa AF: 0.588 Hom.: 40604

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs716392; hg19: chr17-53589413;