chr16-4609808-G-A

Variant names:

• chr16-4609808-G-A
• rs371867321
• NM_145253.3:c.359C>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_145253.3(UBALD1):​c.359C>T​(p.Ala120Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000684 in 1,520,570 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000071 (1 hom.)
• Consequence: UBALD1 NM_145253.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.23
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.04225096).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145253.3. 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
	UBALD1	NM_145253.3	MANE Select	c.359C>T	p.Ala120Val	missense	Exon 3 of 3	NP_660296.1	Q8TB05-1
	UBALD1	NM_001330467.2		c.284C>T	p.Ala95Val	missense	Exon 3 of 3	NP_001317396.1	K7EM88
	UBALD1	NM_001411032.1		c.*175C>T		3_prime_UTR	Exon 3 of 3	NP_001397961.1	K7EKR5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBALD1	ENST00000283474.12	TSL:1 MANE Select	c.359C>T	p.Ala120Val	missense	Exon 3 of 3	ENSP00000283474.6	Q8TB05-1
	UBALD1	ENST00000590891.1	TSL:6	c.464C>T	p.Ala155Val	missense	Exon 1 of 1	ENSP00000465706.1	Q8TB05-2
	UBALD1	ENST00000591401.5	TSL:5	c.296C>T	p.Ala99Val	missense	Exon 2 of 2	ENSP00000467671.1	K7EQ49

Frequencies

GnomAD3 genomes AF: 0.0000461 AC: 7 AN: 151922 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000967

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000442

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.0000845 AC: 13 AN: 153924 AF XY: 0.0000951

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.000216

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000289

Gnomad OTH exome AF: 0.000285

GnomAD4 exome AF: 0.0000709 AC: 97 AN: 1368648 Hom.: 1 Cov.: 32 AF XY: 0.0000833 AC XY: 56 AN XY: 672146

African (AFR) AF: 0.0000988 AC: 3 AN: 30366

American (AMR) AF: 0.0000325 AC: 1 AN: 30808

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20288

East Asian (EAS) AF: 0.000210 AC: 8 AN: 38084

South Asian (SAS) AF: 0.000427 AC: 31 AN: 72566

European-Finnish (FIN) AF: 0.0000213 AC: 1 AN: 46902

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5260

European-Non Finnish (NFE) AF: 0.0000496 AC: 53 AN: 1068126

Other (OTH) AF: 0.00 AC: 0 AN: 56248

GnomAD4 genome AF: 0.0000461 AC: 7 AN: 151922 Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2 AN XY: 74200

African (AFR) AF: 0.0000967 AC: 4 AN: 41358

American (AMR) AF: 0.00 AC: 0 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10616

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 316

European-Non Finnish (NFE) AF: 0.0000442 AC: 3 AN: 67922

Other (OTH) AF: 0.00 AC: 0 AN: 2088

Alfa AF: 0.000131 Hom.: 0

Bravo AF: 0.0000529

ESP6500AA AF: 0.000244 AC: 1

ESP6500EA AF: 0.00 AC: 0

ExAC AF: 0.0000852 AC: 10

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.071
BayesDel_addAF	Benign	-0.22	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	14
DANN	Benign	0.80
DEOGEN2	Benign	0.0011	T
Eigen	Benign	-0.80
Eigen_PC	Benign	-0.81
FATHMM_MKL	Benign	0.41	N
LIST_S2	Benign	0.63	T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.042	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	-1.0	N
PhyloP100		4.2
PrimateAI	Uncertain	0.69	T
PROVEAN	Benign	-0.50	N
REVEL	Benign	0.058
Sift	Benign	0.51	T
Sift4G	Benign	0.50	T
Polyphen		0.94	P
Vest4		0.12
MVP		0.25
MPC		0.16
ClinPred		0.014	T
GERP RS		2.8
Varity_R		0.025
gMVP		0.20
Mutation Taster		=90/10	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: rs371867321; hg19: chr16-4659809; COSMIC: COSV52082850; COSMIC: COSV52082850;