rs9329350

chr13-113804266-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182614.4(TMEM255B):c.670-619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 152,182 control chromosomes in the GnomAD database, including 579 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 0.082 (579 hom., cov: 34)
• Consequence: TMEM255B NM_182614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.64

Genes affected

TMEM255B (HGNC:28297): (transmembrane protein 255B) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TMEM255B	NM_182614.4	c.670-619C>T		intron_variant		ENST00000375353.5
TMEM255B	NM_001348663.2	c.669+2454C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM255B	ENST00000375353.5	c.670-619C>T		intron_variant		1	NM_182614.4	P1
TMEM255B	ENST00000467169.1	n.284-619C>T		intron_variant, non_coding_transcript_variant		3
TMEM255B	ENST00000498692.1	n.384-619C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0818 AC: 12438 AN: 152064 Hom.: 580 Cov.: 34

Gnomad AFR AF: 0.0941

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0804

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

GnomAD4 genome AF: 0.0818 AC: 12452 AN: 152182 Hom.: 579 Cov.: 34 AF XY: 0.0835 AC XY: 6214 AN XY: 74394

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.0805

Alfa AF: 0.0711 Hom.: 58

Bravo AF: 0.0859

Asia WGS AF: 0.124 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	3.8
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9329350; hg19: chr13-114507239; COSMIC: COSV64704940; COSMIC: COSV64704940;