rs4151400

Variant names:

• chr14-60961694-C-T
• rs4151400
• NM_002431.4:c.810-6535C>T

Variant summary

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

The NM_002431.4(MNAT1):​c.810-6535C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.91 in 152,228 control chromosomes in the GnomAD database, including 63,710 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 0.91 (63710 hom., cov: 32)
• Consequence: MNAT1 NM_002431.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MNAT1	NM_002431.4	c.810-6535C>T		intron_variant	Intron 7 of 7	ENST00000261245.9	NP_002422.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MNAT1	ENST00000261245.9	c.810-6535C>T		intron_variant	Intron 7 of 7	1	NM_002431.4	ENSP00000261245.4

Frequencies

GnomAD3 genomes AF: 0.911 AC: 138505 AN: 152110 Hom.: 63684 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.990

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.986

Gnomad OTH AF: 0.914

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

GnomAD4 genome AF: 0.910 AC: 138588 AN: 152228 Hom.: 63710 Cov.: 32 AF XY: 0.907 AC XY: 67517 AN XY: 74432

African (AFR) AF: 0.806 AC: 33438 AN: 41496

American (AMR) AF: 0.875 AC: 13380 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3291 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4079 AN: 5172

South Asian (SAS) AF: 0.761 AC: 3672 AN: 4824

European-Finnish (FIN) AF: 0.990 AC: 10497 AN: 10608

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.986 AC: 67122 AN: 68044

Other (OTH) AF: 0.910 AC: 1922 AN: 2112

Alfa AF: 0.933 Hom.: 10846

Bravo AF: 0.900

Asia WGS AF: 0.767 AC: 2667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.3
DANN	Benign	0.62
PhyloP100		0.42
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: rs4151400; hg19: chr14-61428412;