rs13173738

chr5-110651527-G-Achr5-110651527-G-Cchr5-110651527-G-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM232	NM_001039763.4	c.126-9156C>T		intron_variant		ENST00000455884.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM232	ENST00000455884.7	c.126-9156C>T		intron_variant		2	NM_001039763.4	P1

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.782

Gnomad4 OTH AF: 0.593

Alfa AF: 0.718 Hom.: 16038

Bravo AF: 0.550

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.16
Dann	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs13173738; hg19: chr5-109987228;