ENST00000507188.6:n.1308+307C>T

Variant names:

• chr5-110322927-G-A
• rs9326798
• ENST00000507188.6:n.1308+307C>T

Variant summary

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

The ENST00000507188.6(TMEM232):​n.1308+307C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 152,200 control chromosomes in the GnomAD database, including 153 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 0.032 (153 hom., cov: 32)
• Consequence: TMEM232 ENST00000507188.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.346
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.068 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507188.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM232	ENST00000507188.6	TSL:2	n.1308+307C>T		intron	N/A
	ENSG00000303264	ENST00000793266.1		n.263-3425G>A		intron	N/A
	ENSG00000303264	ENST00000793267.1		n.255-3425G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0317 AC: 4822 AN: 152082 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0693

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0716

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0333

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00584

Gnomad OTH AF: 0.0269

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

GnomAD4 genome AF: 0.0317 AC: 4826 AN: 152200 Hom.: 153 Cov.: 32 AF XY: 0.0321 AC XY: 2390 AN XY: 74416

African (AFR) AF: 0.0692 AC: 2875 AN: 41518

American (AMR) AF: 0.0715 AC: 1092 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3470

East Asian (EAS) AF: 0.0391 AC: 202 AN: 5172

South Asian (SAS) AF: 0.0330 AC: 159 AN: 4824

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00584 AC: 397 AN: 68020

Other (OTH) AF: 0.0266 AC: 56 AN: 2104

Alfa AF: 0.00393 Hom.: 1

Bravo AF: 0.0397

Asia WGS AF: 0.0390 AC: 135 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9326798; hg19: chr5-109658628;