rs13360927

Positions:

• chr5-110700055-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039763.4(TMEM232):​c.-13+26572T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0934 in 152,082 control chromosomes in the GnomAD database, including 780 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 0.093 (780 hom., cov: 32)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

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=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM232	NM_001039763.4	c.-13+26572T>C		intron_variant		ENST00000455884.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM232	ENST00000455884.7	c.-13+26572T>C		intron_variant		2	NM_001039763.4	P1

Frequencies

GnomAD3 genomes AF: 0.0934 AC: 14198 AN: 151966 Hom.: 779 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0529

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0988

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0819

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

GnomAD4 genome AF: 0.0934 AC: 14204 AN: 152082 Hom.: 780 Cov.: 32 AF XY: 0.0960 AC XY: 7143 AN XY: 74374

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.0529

Gnomad4 ASJ AF: 0.0782

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.181

Gnomad4 FIN AF: 0.0988

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0731 Hom.: 451

Bravo AF: 0.0853

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.3
DANN	Benign	0.75

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: rs13360927; hg19: chr5-110035756;