Variant 6-37463981-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015050.3(CMTR1):c.1505+973T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,092 control chromosomes in the GnomAD database, including 39,802 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 0.72 ( 39802 hom., cov: 32)

Consequence

CMTR1
NM_015050.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345

Variant links:

Genes affected

CMTR1 (HGNC:21077): (cap methyltransferase 1) Enables mRNA (nucleoside-2'-O-)-methyltransferase activity. Involved in 7-methylguanosine mRNA capping and cap1 mRNA methylation. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

CMTR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
CMTR1	NM_015050.3 link	c.1505+973T>C	intron_variant	ENST00000373451.9	NP_055865.1	Q8N1G2
CMTR1	XM_047418462.1 link	c.1505+973T>C	intron_variant		XP_047274418.1
CMTR1	XM_047418463.1 link	c.1505+973T>C	intron_variant		XP_047274419.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CMTR1	ENST00000373451.9 link	c.1505+973T>C		intron_variant		1	NM_015050.3	ENSP00000362550.4		Q8N1G2

Frequencies

GnomAD3 genomes

AF:

0.718

AC:

109145

AN:

151972

Hom.:

39749

Cov.:

show subpopulations

Gnomad AFR

AF:

0.817

Gnomad AMI

AF:

0.762

Gnomad AMR

AF:

0.726

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.442

Gnomad SAS

AF:

0.575

Gnomad FIN

AF:

0.632

Gnomad MID

AF:

0.816

Gnomad NFE

AF:

0.696

Gnomad OTH

AF:

0.731

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

GnomAD4 genome

AF:

0.718

AC:

109254

AN:

152092

Hom.:

39802

Cov.:

AF XY:

0.711

AC XY:

52813

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.817

Gnomad4 AMR

AF:

0.727

Gnomad4 ASJ

AF:

0.785

Gnomad4 EAS

AF:

0.442

Gnomad4 SAS

AF:

0.576

Gnomad4 FIN

AF:

0.632

Gnomad4 NFE

AF:

0.696

Gnomad4 OTH

AF:

0.726

Alfa

AF:

0.702

Hom.:

77096

Bravo

AF:

0.731

Asia WGS

AF:

0.508

AC:

1766

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.81

DANN

Benign

0.51

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over