chr13-113804266-C-T

Variant names:

• chr13-113804266-C-T
• rs9329350
• NM_182614.4:c.670-619C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TMEM255B	NM_182614.4	c.670-619C>T		intron_variant	Intron 7 of 8	ENST00000375353.5	NP_872420.1
TMEM255B	NM_001348663.2	c.669+2454C>T		intron_variant	Intron 7 of 7		NP_001335592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM255B	ENST00000375353.5	c.670-619C>T		intron_variant	Intron 7 of 8	1	NM_182614.4	ENSP00000364502.3
TMEM255B	ENST00000467169.1	n.284-619C>T		intron_variant	Intron 1 of 2	3
TMEM255B	ENST00000498692.1	n.384-619C>T		intron_variant	Intron 3 of 3	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

African (AFR) AF: 0.0941 AC: 3910 AN: 41536

American (AMR) AF: 0.139 AC: 2133 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0288 AC: 100 AN: 3470

East Asian (EAS) AF: 0.130 AC: 672 AN: 5150

South Asian (SAS) AF: 0.130 AC: 628 AN: 4820

European-Finnish (FIN) AF: 0.0653 AC: 692 AN: 10600

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0593 AC: 4031 AN: 67994

Other (OTH) AF: 0.0805 AC: 170 AN: 2112

Alfa AF: 0.0713 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
PhyloP100		-2.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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