rs13181561

Variant names:

• chr5-139471320-G-A
• rs13181561
• NM_001365197.1:c.9+190G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-139471320-G-A
• chr5-139471320-G-C

Variant summary

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

The NM_001365197.1(SMIM33):​c.9+190G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 151,954 control chromosomes in the GnomAD database, including 29,980 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 0.61 (29980 hom., cov: 31)
• Consequence: SMIM33 NM_001365197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 29 publications found

Genes affected

SMIM33 (HGNC:53645): (small integral membrane protein 33) 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMIM33	NM_001365197.1	c.9+190G>A		intron_variant	Intron 1 of 1	ENST00000637503.2	NP_001352126.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SMIM33	ENST00000637503.2	c.9+190G>A		intron_variant	Intron 1 of 1	5	NM_001365197.1	ENSP00000490796.1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93064 AN: 151836 Hom.: 29968 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.613 AC: 93121 AN: 151954 Hom.: 29980 Cov.: 31 AF XY: 0.609 AC XY: 45203 AN XY: 74236

African (AFR) AF: 0.428 AC: 17745 AN: 41432

American (AMR) AF: 0.583 AC: 8902 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.650 AC: 2257 AN: 3472

East Asian (EAS) AF: 0.374 AC: 1924 AN: 5142

South Asian (SAS) AF: 0.661 AC: 3186 AN: 4820

European-Finnish (FIN) AF: 0.695 AC: 7331 AN: 10542

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.731 AC: 49673 AN: 67960

Other (OTH) AF: 0.620 AC: 1306 AN: 2108

Alfa AF: 0.691 Hom.: 163618

Bravo AF: 0.598

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.52
PhyloP100		-1.5
PromoterAI		-0.0017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs13181561; hg19: chr5-138850905;