rs749015969

Variant names:

• chr16-4609778-G-A
• rs749015969
• NM_145253.3:c.389C>T

Your query was ambiguous. Multiple possible variants found:

• chr16-4609778-G-A
• chr16-4609778-G-C
• chr16-4609778-G-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_145253.3(UBALD1):​c.389C>T​(p.Pro130Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,356,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P130H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: UBALD1 NM_145253.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 0 publications found

Genes affected

UBALD1 (HGNC:29576): (UBA like domain containing 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17694914).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBALD1	NM_145253.3	c.389C>T	p.Pro130Leu	missense_variant	Exon 3 of 3	ENST00000283474.12	NP_660296.1
UBALD1	NM_001330467.2	c.314C>T	p.Pro105Leu	missense_variant	Exon 3 of 3		NP_001317396.1
UBALD1	NM_001411032.1	c.*205C>T		3_prime_UTR_variant	Exon 3 of 3		NP_001397961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBALD1	ENST00000283474.12	c.389C>T	p.Pro130Leu	missense_variant	Exon 3 of 3	1	NM_145253.3	ENSP00000283474.6

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.00000672 AC: 1 AN: 148714 AF XY: 0.0000123

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000143

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000103 AC: 14 AN: 1356540 Hom.: 0 Cov.: 32 AF XY: 0.0000120 AC XY: 8 AN XY: 664888

African (AFR) AF: 0.00 AC: 0 AN: 29666

American (AMR) AF: 0.00 AC: 0 AN: 28296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19626

East Asian (EAS) AF: 0.00 AC: 0 AN: 37730

South Asian (SAS) AF: 0.00 AC: 0 AN: 70332

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46208

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5002

European-Non Finnish (NFE) AF: 0.0000132 AC: 14 AN: 1064080

Other (OTH) AF: 0.00 AC: 0 AN: 55600

GnomAD4 genome Cov.: 32

ExAC AF: 0.00000874 AC: 1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.070
BayesDel_addAF	Benign	-0.082	T
BayesDel_noAF	Benign	-0.36
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Benign	0.13	.;.;T;T;.
Eigen	Benign	-0.12
Eigen_PC	Benign	-0.035
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Uncertain	0.88	D;D;D;D;D
M_CAP	Uncertain	0.16	D
MetaRNN	Benign	0.18	T;T;T;T;T
MetaSVM	Benign	-0.66	T
MutationAssessor	Benign	1.9	.;.;L;.;.
PhyloP100		1.9
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-3.4	.;.;D;.;.
REVEL	Benign	0.13
Sift	Uncertain	0.0030	.;.;D;.;.
Sift4G	Uncertain	0.010	D;D;D;D;T
Polyphen		0.0040, 0.011	.;.;B;B;.
Vest4		0.19
MutPred		0.23		.;.;Loss of glycosylation at P130 (P = 0.03);.;.;
MVP		0.17
MPC		0.16
ClinPred		0.79	D
GERP RS		4.1
Varity_R		0.19
gMVP		0.36
Mutation Taster		=81/19	polymorphism

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: rs749015969; hg19: chr16-4659779;