rs7640978

chr3-32491518-C-T

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CMTM6	NM_017801.3	c.315+192G>A		intron_variant		ENST00000205636.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CMTM6	ENST00000205636.4	c.315+192G>A		intron_variant		1	NM_017801.3	P1
CMTM6	ENST00000495177.1	n.366+192G>A		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.0894

Gnomad4 ASJ AF: 0.0848

Gnomad4 EAS AF: 0.0603

Gnomad4 SAS AF: 0.0327

Gnomad4 FIN AF: 0.0898

Gnomad4 NFE AF: 0.0861

Gnomad4 OTH AF: 0.126

Alfa AF: 0.0931 Hom.: 1359

Bravo AF: 0.145

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	6.1
Dann	Benign	0.62

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: rs7640978; hg19: chr3-32533010;