chr3-32288005-C-T

Position:

• chr3-32288005-C-T

Variant summary

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

The ENST00000307526.4(CMTM8):​c.147+48886C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,030 control chromosomes in the GnomAD database, including 5,419 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 0.26 (5419 hom., cov: 33)
• Consequence: CMTM8 ENST00000307526.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.330

Genes affected

CMTM8 (HGNC:19179): (CKLF like MARVEL transmembrane domain containing 8) This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and the transmembrane 4 superfamilies. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 3. This gene acts as a tumor suppressor, and plays a role in regulating the migration of tumor cells. The encoded protein is thought to function as a a negative regulator of epidermal growth factor-induced signaling. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CMTM8	NM_178868.5	c.147+48886C>T		intron_variant		ENST00000307526.4	NP_849199.2
CMTM8	NM_001320308.2	c.147+48886C>T		intron_variant			NP_001307237.1
CMTM8	XM_011533416.4	c.216+5346C>T		intron_variant			XP_011531718.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMTM8	ENST00000307526.4	c.147+48886C>T		intron_variant		1	NM_178868.5	ENSP00000307741	P1
CMTM8	ENST00000458535.6	c.147+48886C>T		intron_variant		1		ENSP00000412934

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39491 AN: 151912 Hom.: 5413 Cov.: 33

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0813

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.260 AC: 39524 AN: 152030 Hom.: 5419 Cov.: 33 AF XY: 0.257 AC XY: 19097 AN XY: 74314

Gnomad4 AFR AF: 0.288

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0819

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.223

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.258

Alfa AF: 0.244 Hom.: 10176

Bravo AF: 0.271

Asia WGS AF: 0.137 AC: 475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.79

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: rs4380451; hg19: chr3-32329497;