chr13-113792362-C-A

Variant names:

• chr13-113792362-C-A
• rs7491764
• NM_182614.4:c.253-2786C>A

Variant summary

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

The NM_182614.4(TMEM255B):​c.253-2786C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 152,172 control chromosomes in the GnomAD database, including 14,093 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 0.41 (14093 hom., cov: 34)
• Consequence: TMEM255B NM_182614.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 4 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TMEM255B	NM_182614.4	c.253-2786C>A		intron_variant	Intron 3 of 8	ENST00000375353.5	NP_872420.1
TMEM255B	NM_001348663.2	c.253-2786C>A		intron_variant	Intron 3 of 7		NP_001335592.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TMEM255B	ENST00000375353.5	c.253-2786C>A		intron_variant	Intron 3 of 8	1	NM_182614.4	ENSP00000364502.3
TMEM255B	ENST00000488362.5	c.253-2786C>A		intron_variant	Intron 3 of 4	2		ENSP00000479391.1
TMEM255B	ENST00000375348.3	n.277-2786C>A		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62159 AN: 152052 Hom.: 14085 Cov.: 34

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.409 AC: 62190 AN: 152172 Hom.: 14093 Cov.: 34 AF XY: 0.418 AC XY: 31112 AN XY: 74418

African (AFR) AF: 0.227 AC: 9445 AN: 41534

American (AMR) AF: 0.465 AC: 7120 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 898 AN: 3468

East Asian (EAS) AF: 0.721 AC: 3734 AN: 5178

South Asian (SAS) AF: 0.561 AC: 2707 AN: 4826

European-Finnish (FIN) AF: 0.553 AC: 5856 AN: 10588

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 31005 AN: 67972

Other (OTH) AF: 0.389 AC: 818 AN: 2104

Alfa AF: 0.321 Hom.: 1180

Bravo AF: 0.397

Asia WGS AF: 0.636 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.19
PhyloP100		-1.8
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: rs7491764; hg19: chr13-114495335;