chr16-23570832-G-A

Variant names:

• chr16-23570832-G-A
• rs1610
• NM_019116.3:c.*242G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_019116.3(UBFD1):​c.*242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 335,370 control chromosomes in the GnomAD database, including 4,480 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 (1799 hom., cov: 31)
  • Exomes 𝑓: 0.16 (2681 hom.)
• Consequence: UBFD1 NM_019116.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.228
• Publications: 22 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=-0.67).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBFD1	NM_019116.3	c.*242G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000395878.8	NP_061989.2
UBFD1	XM_011545894.4	c.*201G>A		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.*242G>A		3_prime_UTR_variant	Exon 7 of 7	2	NM_019116.3	ENSP00000379217.3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22090 AN: 151626 Hom.: 1797 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.160 AC: 29403 AN: 183624 Hom.: 2681 Cov.: 0 AF XY: 0.162 AC XY: 15569 AN XY: 96004

African (AFR) AF: 0.0988 AC: 550 AN: 5568

American (AMR) AF: 0.137 AC: 890 AN: 6516

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 670 AN: 6294

East Asian (EAS) AF: 0.292 AC: 3678 AN: 12580

South Asian (SAS) AF: 0.201 AC: 2891 AN: 14406

European-Finnish (FIN) AF: 0.211 AC: 2316 AN: 10984

Middle Eastern (MID) AF: 0.132 AC: 116 AN: 878

European-Non Finnish (NFE) AF: 0.144 AC: 16598 AN: 114934

Other (OTH) AF: 0.148 AC: 1694 AN: 11464

GnomAD4 genome AF: 0.146 AC: 22109 AN: 151746 Hom.: 1799 Cov.: 31 AF XY: 0.150 AC XY: 11120 AN XY: 74136

African (AFR) AF: 0.103 AC: 4258 AN: 41352

American (AMR) AF: 0.133 AC: 2023 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 386 AN: 3464

East Asian (EAS) AF: 0.287 AC: 1485 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4806

European-Finnish (FIN) AF: 0.223 AC: 2335 AN: 10448

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

European-Non Finnish (NFE) AF: 0.149 AC: 10118 AN: 67946

Other (OTH) AF: 0.140 AC: 293 AN: 2100

Alfa AF: 0.141 Hom.: 2020

Bravo AF: 0.136

Asia WGS AF: 0.219 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	11
DANN	Benign	0.80
PhyloP100		0.23
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: rs1610; hg19: chr16-23582153;