5-110651527-G-A

Variant names:

• chr5-110651527-G-A
• rs13173738
• NM_001039763.4:c.126-9156C>T

Variant summary

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

The NM_001039763.4(TMEM232):​c.126-9156C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,820 control chromosomes in the GnomAD database, including 30,828 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 0.58 (30828 hom., cov: 30)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 3 publications found

Genes affected

TMEM232 (HGNC:37270): (transmembrane protein 232) 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=-1.07).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039763.4. 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
	TMEM232	NM_001039763.4	MANE Select	c.126-9156C>T		intron	N/A	NP_001034852.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM232	ENST00000455884.7	TSL:2 MANE Select	c.126-9156C>T		intron	N/A	ENSP00000401477.2
	TMEM232	ENST00000512003.7	TSL:1	n.125+15701C>T		intron	N/A	ENSP00000427785.2
	TMEM232	ENST00000515518.6	TSL:1	n.46-9156C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87769 AN: 151700 Hom.: 30823 Cov.: 30

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.782

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.578 AC: 87771 AN: 151820 Hom.: 30828 Cov.: 30 AF XY: 0.578 AC XY: 42883 AN XY: 74154

African (AFR) AF: 0.159 AC: 6574 AN: 41408

American (AMR) AF: 0.637 AC: 9710 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2489 AN: 3464

East Asian (EAS) AF: 0.493 AC: 2529 AN: 5132

South Asian (SAS) AF: 0.679 AC: 3267 AN: 4810

European-Finnish (FIN) AF: 0.751 AC: 7906 AN: 10528

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.782 AC: 53121 AN: 67922

Other (OTH) AF: 0.593 AC: 1248 AN: 2106

Alfa AF: 0.716 Hom.: 18284

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.16
DANN	Benign	0.40
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs13173738; hg19: chr5-109987228;