17-76265611-C-T

Variant names:

• chr17-76265611-C-T
• NM_182565.4:c.106C>T

Variant summary

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

The NM_182565.4(UBALD2):​c.106C>T​(p.His36Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: UBALD2 NM_182565.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.49
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

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.106C>T	p.His36Tyr	missense	Exon 1 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.106C>T	p.His36Tyr	missense	Exon 1 of 3	ENSP00000331298.6	Q8IYN6
	UBALD2	ENST00000864754.1		c.106C>T	p.His36Tyr	missense	Exon 1 of 2	ENSP00000534813.1
	UBALD2	ENST00000587913.1	TSL:3	c.-61+208C>T		intron	N/A	ENSP00000468297.1	K7ERK7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1148806 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 567322

African (AFR) AF: 0.00 AC: 0 AN: 22804

American (AMR) AF: 0.00 AC: 0 AN: 24894

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16002

East Asian (EAS) AF: 0.00 AC: 0 AN: 18420

South Asian (SAS) AF: 0.00 AC: 0 AN: 52882

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2854

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 936404

Other (OTH) AF: 0.00 AC: 0 AN: 42122

GnomAD4 genome Cov.: 33

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	Pathogenic	0.76
BayesDel_addAF	Uncertain	0.079	D
BayesDel_noAF	Benign	-0.12
CADD	Pathogenic	26
DANN	Uncertain	0.99
DEOGEN2	Benign	0.30	T
Eigen	Uncertain	0.27
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.85	D
LIST_S2	Uncertain	0.96	D
M_CAP	Pathogenic	0.91	D
MetaRNN	Uncertain	0.63	D
MetaSVM	Benign	-0.59	T
MutationAssessor	Uncertain	2.3	M
PhyloP100		4.5
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-4.7	D
REVEL	Benign	0.22
Sift	Uncertain	0.0030	D
Sift4G	Uncertain	0.015	D
Polyphen		0.78	P
Vest4		0.53
MutPred		0.51		Loss of disorder (P = 0.2692)
MVP		0.29
MPC		2.0
ClinPred		0.99	D
GERP RS		2.5
PromoterAI		0.23	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.73
gMVP		0.94

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

hg19: chr17-74261692;