chr3-32491518-C-T

Variant names:

• chr3-32491518-C-T
• rs7640978
• NM_017801.3:c.315+192G>A

Variant summary

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

The NM_017801.3(CMTM6):​c.315+192G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,146 control chromosomes in the GnomAD database, including 2,076 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 0.14 (2076 hom., cov: 32)
• Consequence: CMTM6 NM_017801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 59 publications found

Genes affected

CMTM6 (HGNC:19177): (CKLF like MARVEL transmembrane domain containing 6) This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and transmembrane 4 superfamilies. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 3. This gene is widely expressed in many tissues, but the exact function of the encoded protein is unknown. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017801.3. 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
	CMTM6	NM_017801.3	MANE Select	c.315+192G>A		intron	N/A	NP_060271.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CMTM6	ENST00000205636.4	TSL:1 MANE Select	c.315+192G>A		intron	N/A	ENSP00000205636.3
	CMTM6	ENST00000495177.1	TSL:2	n.366+192G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20803 AN: 152028 Hom.: 2074 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0895

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.0604

Gnomad SAS AF: 0.0329

Gnomad FIN AF: 0.0898

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.137 AC: 20826 AN: 152146 Hom.: 2076 Cov.: 32 AF XY: 0.134 AC XY: 9984 AN XY: 74378

African (AFR) AF: 0.278 AC: 11529 AN: 41470

American (AMR) AF: 0.0894 AC: 1366 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3466

East Asian (EAS) AF: 0.0603 AC: 312 AN: 5170

South Asian (SAS) AF: 0.0327 AC: 158 AN: 4828

European-Finnish (FIN) AF: 0.0898 AC: 952 AN: 10604

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0861 AC: 5853 AN: 68006

Other (OTH) AF: 0.126 AC: 266 AN: 2110

Alfa AF: 0.101 Hom.: 3482

Bravo AF: 0.145

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.62
PhyloP100		0.12
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: rs7640978; hg19: chr3-32533010;