chr14-60905092-G-A

Variant names:

• chr14-60905092-G-A
• rs2225199
• NM_002431.4:c.809+25257G>A

Variant summary

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

The NM_002431.4(MNAT1):​c.809+25257G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 151,364 control chromosomes in the GnomAD database, including 65,190 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 (65190 hom., cov: 27)
• Consequence: MNAT1 NM_002431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.555
• Publications: 2 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]

ENSG00000258892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002431.4. 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
	MNAT1	NM_002431.4	MANE Select	c.809+25257G>A		intron	N/A	NP_002422.1
	MNAT1	NM_001177963.2		c.683+25257G>A		intron	N/A	NP_001171434.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MNAT1	ENST00000261245.9	TSL:1 MANE Select	c.809+25257G>A		intron	N/A	ENSP00000261245.4
	MNAT1	ENST00000539616.6	TSL:1	c.683+25257G>A		intron	N/A	ENSP00000446437.2
	MNAT1	ENST00000554002.5	TSL:3	c.494+25257G>A		intron	N/A	ENSP00000451379.1

Frequencies

GnomAD3 genomes AF: 0.924 AC: 139819 AN: 151246 Hom.: 65158 Cov.: 27

Gnomad AFR AF: 0.801

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.952

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.876

Gnomad FIN AF: 0.993

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.924 AC: 139909 AN: 151364 Hom.: 65190 Cov.: 27 AF XY: 0.923 AC XY: 68278 AN XY: 73956

African (AFR) AF: 0.801 AC: 32918 AN: 41072

American (AMR) AF: 0.947 AC: 14380 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.952 AC: 3305 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4172 AN: 5112

South Asian (SAS) AF: 0.877 AC: 4198 AN: 4786

European-Finnish (FIN) AF: 0.993 AC: 10446 AN: 10524

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67352 AN: 67918

Other (OTH) AF: 0.931 AC: 1943 AN: 2088

Alfa AF: 0.967 Hom.: 267995

Bravo AF: 0.918

Asia WGS AF: 0.851 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.40
PhyloP100		0.56
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: rs2225199; hg19: chr14-61371810;