rs10067777

chr5-110490595-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.1703+37993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 152,132 control chromosomes in the GnomAD database, including 539 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 0.076 (539 hom., cov: 32)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM232	NM_001039763.4	c.1703+37993T>C		intron_variant		ENST00000455884.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM232	ENST00000455884.7	c.1703+37993T>C		intron_variant		2	NM_001039763.4	P1
TMEM232	ENST00000512003.7	c.*998-65679T>C		intron_variant, NMD_transcript_variant		1
TMEM232	ENST00000515518.6	n.1376-65679T>C		intron_variant, non_coding_transcript_variant		1
TMEM232	ENST00000508571.6	n.1018+77852T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11558 AN: 152012 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0760 AC: 11557 AN: 152132 Hom.: 539 Cov.: 32 AF XY: 0.0799 AC XY: 5942 AN XY: 74368

Gnomad4 AFR AF: 0.0659

Gnomad4 AMR AF: 0.0480

Gnomad4 ASJ AF: 0.0782

Gnomad4 EAS AF: 0.161

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0786 Hom.: 289

Bravo AF: 0.0656

Asia WGS AF: 0.182 AC: 632 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.3
Dann	Benign	0.52

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: rs10067777; hg19: chr5-109826296;