rs756767078

Variant names:

• chr17-76270375-C-A
• rs756767078
• NM_182565.4:c.365C>A

Your query was ambiguous. Multiple possible variants found:

• chr17-76270375-C-A
• chr17-76270375-C-T

Variant summary

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

The NM_182565.4(UBALD2):​c.365C>A​(p.Ala122Glu) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. A122V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBALD2 NM_182565.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.98
• Publications: 2 publications found

Genes affected

UBALD2 (HGNC:28438): (UBA like domain containing 2)

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=0.07431641).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182565.4. 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
	UBALD2	NM_182565.4	MANE Select	c.365C>A	p.Ala122Glu	missense	Exon 3 of 3	NP_872371.1	Q8IYN6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UBALD2	ENST00000327490.8	TSL:1 MANE Select	c.365C>A	p.Ala122Glu	missense	Exon 3 of 3	ENSP00000331298.6	Q8IYN6
	UBALD2	ENST00000864754.1		c.302C>A	p.Ala101Glu	missense	Exon 2 of 2	ENSP00000534813.1
	UBALD2	ENST00000589240.1	TSL:2	c.185C>A	p.Ala62Glu	missense	Exon 2 of 2	ENSP00000466518.1	K7EMI7

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1392676 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 687714

African (AFR) AF: 0.00 AC: 0 AN: 31838

American (AMR) AF: 0.00 AC: 0 AN: 36192

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25164

East Asian (EAS) AF: 0.00 AC: 0 AN: 36200

South Asian (SAS) AF: 0.00 AC: 0 AN: 79602

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40356

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4184

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1081200

Other (OTH) AF: 0.00 AC: 0 AN: 57940

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.16
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.41
CADD	Benign	15
DANN	Benign	0.91
DEOGEN2	Benign	0.020	T
Eigen	Benign	-0.70
Eigen_PC	Benign	-0.61
FATHMM_MKL	Uncertain	0.89	D
LIST_S2	Benign	0.82	T
M_CAP	Benign	0.033	D
MetaRNN	Benign	0.074	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.69	N
PhyloP100		4.0
PrimateAI	Uncertain	0.50	T
PROVEAN	Benign	-1.1	N
REVEL	Benign	0.063
Sift	Benign	0.66	T
Sift4G	Benign	0.78	T
Polyphen		0.036	B
Vest4		0.21
MutPred		0.14		Gain of catalytic residue at A122 (P = 0.0148)
MVP		0.076
MPC		2.0
ClinPred		0.47	T
GERP RS		0.82
Varity_R		0.075
gMVP		0.33
Mutation Taster		=82/18	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: rs756767078; hg19: chr17-74266456;