rs879284

Positions:

• chr9-35829034-G-A
• chr9-35829034-G-T

Variant summary

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

The ENST00000377996.5(TMEM8B):​c.-450-12100G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 151,948 control chromosomes in the GnomAD database, including 3,577 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 0.21 (3577 hom., cov: 30)
• Consequence: TMEM8B ENST00000377996.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TMEM8B	ENST00000377996.5	c.-450-12100G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31876 AN: 151830 Hom.: 3574 Cov.: 30

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.210 AC: 31881 AN: 151948 Hom.: 3577 Cov.: 30 AF XY: 0.210 AC XY: 15581 AN XY: 74266

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.174

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.213

Alfa AF: 0.198 Hom.: 1267

Bravo AF: 0.221

Asia WGS AF: 0.263 AC: 913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879284; hg19: chr9-35829031; COSMIC: COSV65073989; COSMIC: COSV65073989;