5-110713253-G-A

Position:

• chr5-110713253-G-A

Variant summary

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

The NM_001039763.4(TMEM232):​c.-13+13374C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0941 in 152,124 control chromosomes in the GnomAD database, including 806 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 0.094 (806 hom., cov: 32)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.561

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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM232	NM_001039763.4	c.-13+13374C>T		intron_variant		ENST00000455884.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM232	ENST00000455884.7	c.-13+13374C>T		intron_variant		2	NM_001039763.4	P1

Frequencies

GnomAD3 genomes AF: 0.0942 AC: 14318 AN: 152008 Hom.: 806 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0989

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0703

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0941 AC: 14321 AN: 152124 Hom.: 806 Cov.: 32 AF XY: 0.0970 AC XY: 7216 AN XY: 74380

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0989

Gnomad4 NFE AF: 0.0703

Gnomad4 OTH AF: 0.0839

Alfa AF: 0.0836 Hom.: 331

Bravo AF: 0.0853

Asia WGS AF: 0.189 AC: 652 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.10
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs13361382; hg19: chr5-110048954;