3-109916812-C-T

Variant names:

• chr3-109916812-C-T
• rs605795
• ENST00000488231.1:n.129G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000488231.1(NFYBP1):​n.129G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 747,788 control chromosomes in the GnomAD database, including 157,659 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 0.62 (29240 hom., cov: 32)
  • Exomes 𝑓: 0.65 (128419 hom.)
• Consequence: NFYBP1 ENST00000488231.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.665

Genes affected

NFYBP1 (HGNC:54604): (NFYB pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFYBP1		n.109916812C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NFYBP1	ENST00000488231.1	n.129G>A		non_coding_transcript_exon_variant	Exon 1 of 2	6

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94068 AN: 151852 Hom.: 29204 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 0.655 AC: 390029 AN: 595818 Hom.: 128419 Cov.: 5 AF XY: 0.658 AC XY: 213663 AN XY: 324584

Gnomad4 AFR exome AF: 0.560

Gnomad4 AMR exome AF: 0.665

Gnomad4 ASJ exome AF: 0.688

Gnomad4 EAS exome AF: 0.715

Gnomad4 SAS exome AF: 0.707

Gnomad4 FIN exome AF: 0.575

Gnomad4 NFE exome AF: 0.651

Gnomad4 OTH exome AF: 0.651

GnomAD4 genome AF: 0.620 AC: 94158 AN: 151970 Hom.: 29240 Cov.: 32 AF XY: 0.621 AC XY: 46139 AN XY: 74292

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.617

Alfa AF: 0.649 Hom.: 63778

Bravo AF: 0.621

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.2
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs605795; hg19: chr3-109635659;