rs7701890

Positions:

• chr5-110523120-A-G
• chr5-110523120-A-T

Variant summary

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

The NM_001039763.4(TMEM232):​c.1703+5468T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,054 control chromosomes in the GnomAD database, including 2,103 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 0.15 (2103 hom., cov: 32)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

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 (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM232	NM_001039763.4	c.1703+5468T>C		intron_variant		ENST00000455884.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM232	ENST00000455884.7	c.1703+5468T>C		intron_variant		2	NM_001039763.4	P1
TMEM232	ENST00000512003.7	c.*997+45327T>C		intron_variant, NMD_transcript_variant		1
TMEM232	ENST00000515518.6	n.1375+45327T>C		intron_variant, non_coding_transcript_variant		1
TMEM232	ENST00000508571.6	n.1018+45327T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22674 AN: 151934 Hom.: 2099 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.0948

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0958

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.149 AC: 22697 AN: 152054 Hom.: 2103 Cov.: 32 AF XY: 0.151 AC XY: 11226 AN XY: 74306

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.0933

Gnomad4 ASJ AF: 0.0948

Gnomad4 EAS AF: 0.170

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0958

Gnomad4 OTH AF: 0.151

Alfa AF: 0.105 Hom.: 1195

Bravo AF: 0.145

Asia WGS AF: 0.206 AC: 715 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	2.1
DANN	Benign	0.58

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: rs7701890; hg19: chr5-109858821;