rs10894147

Variant names:

• chr11-129828961-C-G
• rs10894147
• NM_138788.5:c.-9+13063C>G

Your query was ambiguous. Multiple possible variants found:

• chr11-129828961-C-G
• chr11-129828961-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138788.5(TMEM45B):​c.-9+13063C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: TMEM45B NM_138788.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• Publications: 18 publications found

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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138788.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM45B	NM_138788.5	MANE Select	c.-9+13063C>G		intron	N/A	NP_620143.1
	TMEM45B	NM_001331210.2		c.-158-10592C>G		intron	N/A	NP_001318139.1
	TMEM45B	NM_001331211.2		c.-64+13063C>G		intron	N/A	NP_001318140.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM45B	ENST00000281441.8	TSL:2 MANE Select	c.-9+13063C>G		intron	N/A	ENSP00000281441.3
	TMEM45B	ENST00000527754.1	TSL:5	n.143+708C>G		intron	N/A
	TMEM45B	ENST00000529381.1	TSL:2	n.28+13063C>G		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.39
PhyloP100		0.071

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10894147; hg19: chr11-129698856;