rs7491764

chr13-113792362-C-Achr13-113792362-C-Gchr13-113792362-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.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

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=-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/exons	MANE	UniProt
TMEM255B	NM_182614.4	c.253-2786C>A		intron_variant		ENST00000375353.5
TMEM255B	NM_001348663.2	c.253-2786C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM255B	ENST00000375353.5	c.253-2786C>A		intron_variant		1	NM_182614.4	P1
TMEM255B	ENST00000488362.5	c.253-2786C>A		intron_variant		2
TMEM255B	ENST00000375348.3	n.277-2786C>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.259

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.389

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs7491764; hg19: chr13-114495335;