17-55491523-G-A

Variant names:

• chr17-55491523-G-A
• rs4471745
• NM_001395421.2:c.*175-11943C>T

Variant summary

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

The NM_001395421.2(SMIM36):​c.*175-11943C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,082 control chromosomes in the GnomAD database, including 367 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 0.065 (367 hom., cov: 31)
• Consequence: SMIM36 NM_001395421.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 7 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395421.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM36	NM_001395421.2	MANE Select	c.*175-11943C>T		intron	N/A	NP_001382350.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SMIM36	ENST00000636752.2	TSL:5 MANE Select	c.*175-11943C>T		intron	N/A	ENSP00000490644.1
	SMIM36	ENST00000577089.1	TSL:3	n.61-12710C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9857 AN: 151964 Hom.: 351 Cov.: 31

Gnomad AFR AF: 0.0651

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0970

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0651 AC: 9896 AN: 152082 Hom.: 367 Cov.: 31 AF XY: 0.0629 AC XY: 4679 AN XY: 74330

African (AFR) AF: 0.0652 AC: 2708 AN: 41504

American (AMR) AF: 0.0410 AC: 626 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5160

South Asian (SAS) AF: 0.0981 AC: 471 AN: 4802

European-Finnish (FIN) AF: 0.0473 AC: 500 AN: 10572

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0690 AC: 4692 AN: 67988

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0676 Hom.: 1223

Bravo AF: 0.0627

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.46
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs4471745; hg19: chr17-53568884;