11-129828961-C-T

Position:

• chr11-129828961-C-T

Variant summary

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

The NM_138788.5(TMEM45B):​c.-9+13063C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,216 control chromosomes in the GnomAD database, including 863 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 0.11 (863 hom., cov: 33)
• Consequence: TMEM45B NM_138788.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

TMEM45B (HGNC:25194): (transmembrane protein 45B) 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.116 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TMEM45B	NM_138788.5	c.-9+13063C>T		intron_variant		ENST00000281441.8	NP_620143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TMEM45B	ENST00000281441.8	c.-9+13063C>T		intron_variant		2	NM_138788.5	ENSP00000281441	P1
TMEM45B	ENST00000527754.1	n.143+708C>T		intron_variant, non_coding_transcript_variant		5
TMEM45B	ENST00000529381.1	n.28+13063C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15974 AN: 152098 Hom.: 862 Cov.: 33

Gnomad AFR AF: 0.0832

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.105 AC: 15986 AN: 152216 Hom.: 863 Cov.: 33 AF XY: 0.105 AC XY: 7794 AN XY: 74420

Gnomad4 AFR AF: 0.0832

Gnomad4 AMR AF: 0.120

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0991

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.0909

Alfa AF: 0.111 Hom.: 1299

Bravo AF: 0.106

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.9
DANN	Benign	0.40

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: rs10894147; hg19: chr11-129698856;