NM_014176.4:c.469-203T>C

Variant names:

• chr1-202332163-A-G
• rs788801
• NM_014176.4:c.469-203T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_014176.4(UBE2T):​c.469-203T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 152,082 control chromosomes in the GnomAD database, including 8,901 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.34 (8901 hom., cov: 32)
• Consequence: UBE2T NM_014176.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.04
• Publications: 1 publications found

Genes affected

UBE2T (HGNC:25009): (ubiquitin conjugating enzyme E2 T) The protein encoded by this gene catalyzes the covalent attachment of ubiquitin to protein substrates. Defects in this gene have been associated with Fanconi anemia of complementation group T. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]

UBE2T Gene-Disease associations (from GenCC):

• Fanconi anemia complementation group T

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
• Fanconi anemia

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 1-202332163-A-G is Benign according to our data. Variant chr1-202332163-A-G is described in ClinVar as [Benign]. Clinvar id is 1252839.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UBE2T	NM_014176.4	c.469-203T>C		intron_variant	Intron 6 of 6	ENST00000646651.1	NP_054895.1
UBE2T	NM_001310326.2	c.379-203T>C		intron_variant	Intron 6 of 6		NP_001297255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UBE2T	ENST00000646651.1	c.469-203T>C		intron_variant	Intron 6 of 6		NM_014176.4	ENSP00000494957.1

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51597 AN: 151964 Hom.: 8894 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.346

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.339 AC: 51629 AN: 152082 Hom.: 8901 Cov.: 32 AF XY: 0.341 AC XY: 25366 AN XY: 74352

African (AFR) AF: 0.358 AC: 14863 AN: 41498

American (AMR) AF: 0.261 AC: 3987 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.421 AC: 1462 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1192 AN: 5182

South Asian (SAS) AF: 0.270 AC: 1303 AN: 4822

European-Finnish (FIN) AF: 0.367 AC: 3879 AN: 10556

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23628 AN: 67966

Other (OTH) AF: 0.346 AC: 731 AN: 2114

Alfa AF: 0.347 Hom.: 5957

Bravo AF: 0.335

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 15, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.2
DANN	Benign	0.84
PhyloP100		1.0
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: rs788801; hg19: chr1-202301291;