3-109916812-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488231.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFYBP1	ENST00000488231.1	TSL:6	n.129G>A		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AF: 0.560 AC: 9504 AN: 16978

American (AMR) AF: 0.665 AC: 28102 AN: 42252

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 13367 AN: 19418

East Asian (EAS) AF: 0.715 AC: 25025 AN: 35008

South Asian (SAS) AF: 0.707 AC: 48917 AN: 69224

European-Finnish (FIN) AF: 0.575 AC: 28083 AN: 48816

Middle Eastern (MID) AF: 0.652 AC: 2087 AN: 3200

European-Non Finnish (NFE) AF: 0.651 AC: 215043 AN: 330344

Other (OTH) AF: 0.651 AC: 19901 AN: 30578

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

African (AFR) AF: 0.553 AC: 22907 AN: 41400

American (AMR) AF: 0.640 AC: 9773 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2342 AN: 3472

East Asian (EAS) AF: 0.704 AC: 3629 AN: 5158

South Asian (SAS) AF: 0.709 AC: 3419 AN: 4820

European-Finnish (FIN) AF: 0.570 AC: 6015 AN: 10554

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.649 AC: 44107 AN: 67976

Other (OTH) AF: 0.617 AC: 1304 AN: 2112

Alfa AF: 0.643 Hom.: 90686

Bravo AF: 0.621

Asia WGS AF: 0.719 AC: 2503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.2
DANN	Benign	0.38
PhyloP100		-0.67

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs605795;

hg19: chr3-109635659;