5-110400188-A-G

Variant names:

• chr5-110400188-A-G
• rs10491436
• ENST00000507188.6:n.309-2334T>C

Variant summary

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

The ENST00000507188.6(TMEM232):​n.309-2334T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0641 in 152,168 control chromosomes in the GnomAD database, including 651 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 0.064 (651 hom., cov: 32)
• Consequence: TMEM232 ENST00000507188.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 2 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]

ENSG00000303264 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM232	XR_001742181.2	n.2939-9548T>C		intron_variant	Intron 17 of 17
TMEM232	XR_001742182.2	n.2337-9548T>C		intron_variant	Intron 14 of 15

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM232	ENST00000507188.6	n.309-2334T>C		intron_variant	Intron 2 of 8	2
TMEM232	ENST00000508571.6	n.1019-67263T>C		intron_variant	Intron 5 of 5	2
ENSG00000303264	ENST00000793266.1	n.418-2789A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0639 AC: 9721 AN: 152050 Hom.: 648 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0348

Gnomad ASJ AF: 0.0263

Gnomad EAS AF: 0.00983

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0459

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0580

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

GnomAD4 genome AF: 0.0641 AC: 9747 AN: 152168 Hom.: 651 Cov.: 32 AF XY: 0.0636 AC XY: 4730 AN XY: 74420

African (AFR) AF: 0.167 AC: 6937 AN: 41504

American (AMR) AF: 0.0348 AC: 531 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0263 AC: 91 AN: 3466

East Asian (EAS) AF: 0.00985 AC: 51 AN: 5176

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4824

European-Finnish (FIN) AF: 0.0459 AC: 487 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1376 AN: 68002

Other (OTH) AF: 0.0573 AC: 121 AN: 2110

Alfa AF: 0.0478 Hom.: 115

Bravo AF: 0.0666

Asia WGS AF: 0.0240 AC: 82 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.7
DANN	Benign	0.43
PhyloP100		0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10491436; hg19: chr5-109735889;