14-60841619-T-G

Variant names:

• chr14-60841619-T-G
• rs6573333
• NM_002431.4:c.687+22772T>G

Variant summary

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

The NM_002431.4(MNAT1):​c.687+22772T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,070 control chromosomes in the GnomAD database, including 65,095 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 0.92 (65095 hom., cov: 32)
• Consequence: MNAT1 NM_002431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 12 publications found

Genes affected

MNAT1 (HGNC:7181): (MNAT1 component of CDK activating kinase) The protein encoded by this gene, along with cyclin H and CDK7, forms the CDK-activating kinase (CAK) enzymatic complex. This complex activates several cyclin-associated kinases and can also associate with TFIIH to activate transcription by RNA polymerase II. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MNAT1	NM_002431.4	c.687+22772T>G		intron_variant	Intron 6 of 7	ENST00000261245.9	NP_002422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MNAT1	ENST00000261245.9	c.687+22772T>G		intron_variant	Intron 6 of 7	1	NM_002431.4	ENSP00000261245.4

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140007 AN: 151954 Hom.: 65067 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.932

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

GnomAD4 genome AF: 0.921 AC: 140092 AN: 152070 Hom.: 65095 Cov.: 32 AF XY: 0.920 AC XY: 68426 AN XY: 74370

African (AFR) AF: 0.792 AC: 32793 AN: 41420

American (AMR) AF: 0.944 AC: 14428 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3307 AN: 3472

East Asian (EAS) AF: 0.818 AC: 4227 AN: 5168

South Asian (SAS) AF: 0.877 AC: 4223 AN: 4814

European-Finnish (FIN) AF: 0.993 AC: 10509 AN: 10588

Middle Eastern (MID) AF: 0.973 AC: 286 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67446 AN: 68014

Other (OTH) AF: 0.929 AC: 1961 AN: 2112

Alfa AF: 0.966 Hom.: 214597

Bravo AF: 0.915

Asia WGS AF: 0.852 AC: 2959 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.7
DANN	Benign	0.90
PhyloP100		0.31
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: rs6573333; hg19: chr14-61308337;