9-35829034-G-T

Variant names:

• chr9-35829034-G-T
• rs879284
• ENST00000377996.5:c.-450-12100G>T

Variant summary

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

The ENST00000377996.5(TMEM8B):​c.-450-12100G>T 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: 30)
• Consequence: TMEM8B ENST00000377996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 7 publications found

Genes affected

TMEM8B (HGNC:21427): (transmembrane protein 8B) Involved in cell-matrix adhesion. Located in cell surface and plasma 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=-0.65).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377996.5. 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
	TMEM8B	NM_001042590.4	MANE Select	c.-414G>T		upstream_gene	N/A	NP_001036055.2
	TMEM8B	NM_001363620.1		c.-414G>T		upstream_gene	N/A	NP_001350549.1
	TMEM8B	NM_001042589.3		c.-1213G>T		upstream_gene	N/A	NP_001036054.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TMEM8B	ENST00000377996.5	TSL:2	c.-450-12100G>T		intron	N/A	ENSP00000367235.1
	TMEM8B	ENST00000643932.2	MANE Select	c.-414G>T		upstream_gene	N/A	ENSP00000493496.1
	TMEM8B	ENST00000377991.9	TSL:1	c.-1213G>T		upstream_gene	N/A	ENSP00000367230.4

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 1512

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	13
DANN	Benign	0.89
PhyloP100		2.4
PromoterAI		-0.0057	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs879284; hg19: chr9-35829031;