Variant chr8-35235796-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_080872.4(UNC5D):c.12G>T(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,229,838 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0072 ( 10 hom., cov: 33)

Exomes 𝑓: 0.011 ( 68 hom. )

Consequence

UNC5D
NM_080872.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.14

Variant links:

Genes affected

UNC5D (HGNC:18634): (unc-5 netrin receptor D) Predicted to enable netrin receptor activity. Involved in cell-cell adhesion via plasma-membrane adhesion molecules. Predicted to be located in cell surface and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

UNC5D links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.39).

BP6

Variant 8-35235796-G-T is Benign according to our data. Variant chr8-35235796-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 778358.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.14 with no splicing effect.

BS2

High AC in GnomAd4 at 1100 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC5D	NM_080872.4 linkuse as main transcript	c.12G>T	p.Ala4=	synonymous_variant	1/17	ENST00000404895.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC5D	ENST00000404895.7 linkuse as main transcript	c.12G>T	p.Ala4=	synonymous_variant	1/17	1	NM_080872.4	P4	Q6UXZ4-1
UNC5D	ENST00000416672.5 linkuse as main transcript	c.12G>T	p.Ala4=	synonymous_variant	1/18	5		A1
UNC5D	ENST00000420357.5 linkuse as main transcript	c.12G>T	p.Ala4=	synonymous_variant	1/15	5
UNC5D	ENST00000287272.6 linkuse as main transcript	c.12G>T	p.Ala4=	synonymous_variant	1/16	5

Frequencies

GnomAD3 genomes

AF:

0.00723

AC:

1099

AN:

152092

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00224

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0108

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00227

Gnomad FIN

AF:

0.00942

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.0100

Gnomad OTH

AF:

0.00863

GnomAD3 exomes

AF:

0.00862

AC:

AN:

696

Hom.:

AF XY:

0.00220

AC XY:

AN XY:

454

show subpopulations

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:

0.00787

Gnomad NFE exome

AF:

0.00980

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0107

AC:

11487

AN:

1077638

Hom.:

Cov.:

AF XY:

0.0105

AC XY:

5364

AN XY:

508938

show subpopulations

Gnomad4 AFR exome

AF:

0.00153

Gnomad4 AMR exome

AF:

0.0101

Gnomad4 ASJ exome

AF:

0.00957

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00210

Gnomad4 FIN exome

AF:

0.00798

Gnomad4 NFE exome

AF:

0.0116

Gnomad4 OTH exome

AF:

0.00927

GnomAD4 genome

AF:

0.00723

AC:

1100

AN:

152200

Hom.:

Cov.:

AF XY:

0.00735

AC XY:

547

AN XY:

74396

show subpopulations

Gnomad4 AFR

AF:

0.00224

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00248

Gnomad4 FIN

AF:

0.00942

Gnomad4 NFE

AF:

0.0100

Gnomad4 OTH

AF:

0.00854

Alfa

AF:

0.00299

Hom.:

Bravo

AF:

0.00716

Asia WGS

AF:

0.000867

AC:

AN:

3474

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Benign

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over