16-23571790-T-C

Position:

• chr16-23571790-T-C

Variant summary

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

The NM_019116.3(UBFD1):​c.*1200T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,698 control chromosomes in the GnomAD database, including 1,819 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 0.15 (1811 hom., cov: 33)
  • Exomes 𝑓: 0.21 (8 hom.)
• Consequence: UBFD1 NM_019116.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155

Genes affected

UBFD1 (HGNC:30565): (ubiquitin family domain containing 1) Enables RNA binding activity and cadherin binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBFD1	NM_019116.3	c.*1200T>C		3_prime_UTR_variant	7/7	ENST00000395878.8	NP_061989.2
UBFD1	XM_011545894.4	c.*1159T>C		3_prime_UTR_variant	6/6		XP_011544196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBFD1	ENST00000395878.8	c.*1200T>C		3_prime_UTR_variant	7/7	2	NM_019116.3	ENSP00000379217.3
UBFD1	ENST00000567212.5	c.*1200T>C		3_prime_UTR_variant	7/7	2		ENSP00000456292.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22174 AN: 152146 Hom.: 1809 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.210 AC: 91 AN: 434 Hom.: 8 Cov.: 0 AF XY: 0.225 AC XY: 58 AN XY: 258

Gnomad4 FIN exome AF: 0.215

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.146 AC: 22193 AN: 152264 Hom.: 1811 Cov.: 33 AF XY: 0.150 AC XY: 11158 AN XY: 74432

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.141

Alfa AF: 0.145 Hom.: 1738

Bravo AF: 0.137

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	12
DANN	Benign	0.84

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

Other links and lift over

dbSNP: rs152454; hg19: chr16-23583111;