chr5-110523120-A-G

Variant names:

• chr5-110523120-A-G
• rs7701890
• NM_001039763.4:c.1703+5468T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039763.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM232	NM_001039763.4	MANE Select	c.1703+5468T>C		intron	N/A	NP_001034852.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM232	ENST00000455884.7	TSL:2 MANE Select	c.1703+5468T>C		intron	N/A	ENSP00000401477.2
	TMEM232	ENST00000512003.7	TSL:1	n.*997+45327T>C		intron	N/A	ENSP00000427785.2
	TMEM232	ENST00000515518.6	TSL:1	n.1375+45327T>C		intron	N/A

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

African (AFR) AF: 0.254 AC: 10539 AN: 41470

American (AMR) AF: 0.0933 AC: 1425 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0948 AC: 329 AN: 3470

East Asian (EAS) AF: 0.170 AC: 879 AN: 5172

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4816

European-Finnish (FIN) AF: 0.144 AC: 1519 AN: 10554

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0958 AC: 6510 AN: 67972

Other (OTH) AF: 0.151 AC: 320 AN: 2114

Alfa AF: 0.111 Hom.: 3612

Bravo AF: 0.145

Asia WGS AF: 0.206 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.58
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7701890; hg19: chr5-109858821;