NM_019116.3:c.*1200T>C

Variant names:

• chr16-23571790-T-C
• rs152454
• NM_019116.3:c.*1200T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UBFD1	NM_019116.3	c.*1200T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000395878.8	NP_061989.2
UBFD1	XM_011545894.4	c.*1159T>C		3_prime_UTR_variant	Exon 6 of 6		XP_011544196.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBFD1	ENST00000395878.8	c.*1200T>C		3_prime_UTR_variant	Exon 7 of 7	2	NM_019116.3	ENSP00000379217.3
UBFD1	ENST00000567212.5	c.*1200T>C		3_prime_UTR_variant	Exon 7 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.215 AC: 91 AN: 424

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 6

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

African (AFR) AF: 0.103 AC: 4282 AN: 41564

American (AMR) AF: 0.133 AC: 2027 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 391 AN: 3470

East Asian (EAS) AF: 0.290 AC: 1503 AN: 5186

South Asian (SAS) AF: 0.218 AC: 1052 AN: 4830

European-Finnish (FIN) AF: 0.221 AC: 2335 AN: 10588

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10143 AN: 68016

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.145 Hom.: 2548

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
PhyloP100		0.15
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: rs152454; hg19: chr16-23583111;