5-110490595-A-G

Variant names:

• chr5-110490595-A-G
• rs10067777
• NM_001039763.4:c.1703+37993T>C

Variant summary

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

The ENST00000455884.7(TMEM232):​c.1703+37993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.076 in 152,132 control chromosomes in the GnomAD database, including 539 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 0.076 (539 hom., cov: 32)
• Consequence: TMEM232 ENST00000455884.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350
• Publications: 7 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455884.7. 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+37993T>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+37993T>C		intron	N/A	ENSP00000401477.2
	TMEM232	ENST00000512003.7	TSL:1	n.*998-65679T>C		intron	N/A	ENSP00000427785.2
	TMEM232	ENST00000515518.6	TSL:1	n.1376-65679T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0760 AC: 11558 AN: 152012 Hom.: 537 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0481

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.0712

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

GnomAD4 genome AF: 0.0760 AC: 11557 AN: 152132 Hom.: 539 Cov.: 32 AF XY: 0.0799 AC XY: 5942 AN XY: 74368

African (AFR) AF: 0.0659 AC: 2740 AN: 41560

American (AMR) AF: 0.0480 AC: 732 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0782 AC: 271 AN: 3466

East Asian (EAS) AF: 0.161 AC: 829 AN: 5164

South Asian (SAS) AF: 0.194 AC: 936 AN: 4826

European-Finnish (FIN) AF: 0.107 AC: 1133 AN: 10596

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0688 AC: 4673 AN: 67948

Other (OTH) AF: 0.0728 AC: 154 AN: 2114

Alfa AF: 0.0774 Hom.: 307

Bravo AF: 0.0656

Asia WGS AF: 0.182 AC: 632 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	4.3
DANN	Benign	0.52
PhyloP100		-0.035
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: rs10067777; hg19: chr5-109826296;