rs112439044

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_014223.5(NFYC):​c.387+1159C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000801 in 534,396 control chromosomes in the GnomAD database, including 5 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 0.00049 ( 1 hom., cov: 31)
Exomes 𝑓: 0.00093 ( 4 hom. )

Consequence

NFYC
NM_014223.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.618
Variant links:
Genes affected
NFYC (HGNC:7806): (nuclear transcription factor Y subunit gamma) This gene encodes one subunit of a trimeric complex forming a highly conserved transcription factor that binds with high specificity to CCAAT motifs in the promoters of a variety of genes. The encoded protein, subunit C, forms a tight dimer with the B subunit, a prerequisite for subunit A association. The resulting trimer binds to DNA with high specificity and affinity. Subunits B and C each contain a histone-like motif. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BS2
High AC in GnomAd4 at 74 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NFYCNM_014223.5 linkuse as main transcriptc.387+1159C>T intron_variant ENST00000447388.8 NP_055038.2 Q13952-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NFYCENST00000447388.8 linkuse as main transcriptc.387+1159C>T intron_variant 1 NM_014223.5 ENSP00000404427.3 Q13952-2

Frequencies

GnomAD3 genomes
AF:
0.000486
AC:
74
AN:
152138
Hom.:
1
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.0104
Gnomad SAS
AF:
0.00373
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00125
AC:
314
AN:
250978
Hom.:
3
AF XY:
0.00122
AC XY:
166
AN XY:
135866
show subpopulations
Gnomad AFR exome
AF:
0.0000617
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0116
Gnomad SAS exome
AF:
0.00307
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000353
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.000926
AC:
354
AN:
382140
Hom.:
4
Cov.:
0
AF XY:
0.00102
AC XY:
221
AN XY:
217576
show subpopulations
Gnomad4 AFR exome
AF:
0.0000951
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0118
Gnomad4 SAS exome
AF:
0.00268
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000521
Gnomad4 OTH exome
AF:
0.000539
GnomAD4 genome
AF:
0.000486
AC:
74
AN:
152256
Hom.:
1
Cov.:
31
AF XY:
0.000511
AC XY:
38
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.0105
Gnomad4 SAS
AF:
0.00373
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000151
Hom.:
0
Bravo
AF:
0.000540
Asia WGS
AF:
0.00635
AC:
22
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
CADD
Benign
15
DANN
Benign
0.86
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.0

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.

Other links and lift over

dbSNP: rs112439044; hg19: chr1-41220077; API