chr5-110672513-C-T

Variant names:

• chr5-110672513-C-T
• rs17132261
• NM_001039763.4:c.-12-5149G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001039763.4(TMEM232):​c.-12-5149G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0506 in 152,114 control chromosomes in the GnomAD database, including 412 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 0.051 (412 hom., cov: 32)
• Consequence: TMEM232 NM_001039763.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.253
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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.-12-5149G>A		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.-12-5149G>A		intron	N/A	ENSP00000401477.2
	TMEM232	ENST00000512003.7	TSL:1	n.-12-5149G>A		intron	N/A	ENSP00000427785.2
	TMEM232	ENST00000515518.6	TSL:1	n.46-30142G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0506 AC: 7693 AN: 151996 Hom.: 413 Cov.: 32

Gnomad AFR AF: 0.0827

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.0236

Gnomad FIN AF: 0.0111

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0147

Gnomad OTH AF: 0.0646

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

GnomAD4 genome AF: 0.0506 AC: 7701 AN: 152114 Hom.: 412 Cov.: 32 AF XY: 0.0517 AC XY: 3846 AN XY: 74356

African (AFR) AF: 0.0827 AC: 3431 AN: 41492

American (AMR) AF: 0.0955 AC: 1457 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3472

East Asian (EAS) AF: 0.238 AC: 1228 AN: 5160

South Asian (SAS) AF: 0.0236 AC: 114 AN: 4824

European-Finnish (FIN) AF: 0.0111 AC: 117 AN: 10562

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0147 AC: 998 AN: 68022

Other (OTH) AF: 0.0663 AC: 140 AN: 2112

Alfa AF: 0.0338 Hom.: 776

Bravo AF: 0.0630

Asia WGS AF: 0.128 AC: 441 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.7
DANN	Benign	0.28
PhyloP100		0.25
Mutation Taster		=99/1	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: rs17132261; hg19: chr5-110008214;