chr3-32321506-T-C

Variant names:

• chr3-32321506-T-C
• rs9833771
• NM_178868.5:c.148-35867T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178868.5(CMTM8):​c.148-35867T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 151,936 control chromosomes in the GnomAD database, including 11,459 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 0.38 (11459 hom., cov: 31)
• Consequence: CMTM8 NM_178868.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.871
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178868.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMTM8	NM_178868.5	MANE Select	c.148-35867T>C		intron	N/A	NP_849199.2
	CMTM8	NM_001320308.2		c.148-46366T>C		intron	N/A	NP_001307237.1	Q8IZV2-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMTM8	ENST00000307526.4	TSL:1 MANE Select	c.148-35867T>C		intron	N/A	ENSP00000307741.3	Q8IZV2-1
	CMTM8	ENST00000458535.6	TSL:1	c.148-46366T>C		intron	N/A	ENSP00000412934.2	Q8IZV2-2
	CMTM8	ENST00000867234.1		c.261+10853T>C		intron	N/A	ENSP00000537293.1

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57061 AN: 151818 Hom.: 11461 Cov.: 31

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.376 AC: 57084 AN: 151936 Hom.: 11459 Cov.: 31 AF XY: 0.374 AC XY: 27731 AN XY: 74246

African (AFR) AF: 0.272 AC: 11280 AN: 41410

American (AMR) AF: 0.324 AC: 4942 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 974 AN: 3460

East Asian (EAS) AF: 0.181 AC: 936 AN: 5160

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4818

European-Finnish (FIN) AF: 0.482 AC: 5080 AN: 10548

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30925 AN: 67952

Other (OTH) AF: 0.374 AC: 789 AN: 2110

Alfa AF: 0.412 Hom.: 39998

Bravo AF: 0.358

Asia WGS AF: 0.302 AC: 1053 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.68
PhyloP100		0.87
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9833771; hg19: chr3-32362998;