Variant chr6-167305996-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_018974.4(UNC93A):c.922G>A(p.Val308Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00547 in 1,614,142 control chromosomes in the GnomAD database, including 337 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.027 ( 169 hom., cov: 33)

Exomes 𝑓: 0.0033 ( 168 hom. )

Consequence

UNC93A
NM_018974.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.293

Variant links:

Genes affected

UNC93A (HGNC:12570): (unc-93 homolog A) Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

UNC93A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024167001).

BP6

Variant 6-167305996-G-A is Benign according to our data. Variant chr6-167305996-G-A is described in ClinVar as [Benign]. Clinvar id is 781019.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNC93A	NM_018974.4 linkuse as main transcript	c.922G>A	p.Val308Met	missense_variant	6/8	ENST00000230256.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNC93A	ENST00000230256.8 linkuse as main transcript	c.922G>A	p.Val308Met	missense_variant	6/8	1	NM_018974.4	P1	Q86WB7-1
UNC93A	ENST00000366829.2 linkuse as main transcript	c.796G>A	p.Val266Met	missense_variant	5/7	1			Q86WB7-2

Frequencies

GnomAD3 genomes

AF:

0.0265

AC:

4039

AN:

152136

Hom.:

169

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0894

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.0251

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.000617

Gnomad OTH

AF:

0.0234

GnomAD3 exomes

AF:

0.00780

AC:

1961

AN:

251490

Hom.:

AF XY:

0.00599

AC XY:

814

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.0902

Gnomad AMR exome

AF:

0.00471

Gnomad ASJ exome

AF:

0.0206

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.000653

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000615

Gnomad OTH exome

AF:

0.00521

GnomAD4 exome

AF:

0.00327

AC:

4783

AN:

1461888

Hom.:

168

Cov.:

AF XY:

0.00296

AC XY:

2152

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.0907

Gnomad4 AMR exome

AF:

0.00555

Gnomad4 ASJ exome

AF:

0.0209

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.000603

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000379

Gnomad4 OTH exome

AF:

0.00727

GnomAD4 genome

AF:

0.0266

AC:

4053

AN:

152254

Hom.:

169

Cov.:

AF XY:

0.0255

AC XY:

1896

AN XY:

74452

show subpopulations

Gnomad4 AFR

AF:

0.0895

Gnomad4 AMR

AF:

0.0100

Gnomad4 ASJ

AF:

0.0251

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000828

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000617

Gnomad4 OTH

AF:

0.0232

Alfa

AF:

0.00392

Hom.:

Bravo

AF:

0.0304

TwinsUK

AF:

0.00

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.0894

AC:

394

ESP6500EA

AF:

0.00186

AC:

ExAC

AF:

0.00932

AC:

1132

Asia WGS

AF:

0.00549

AC:

AN:

3478

EpiCase

AF:

0.00115

EpiControl

AF:

0.000533

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.47

BayesDel_noAF

Benign

-0.39

CADD

Benign

2.2

DANN

Benign

0.78

DEOGEN2

Benign

0.0058

T;.

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.057

LIST_S2

Benign

0.73

T;T

MetaRNN

Benign

0.0024

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.96

L;.

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.29

PROVEAN

Benign

-0.10

N;N

REVEL

Benign

0.081

Sift

Benign

0.17

T;T

Sift4G

Benign

0.21

T;T

Polyphen

0.14

B;.

Vest4

0.10

MVP

0.21

MPC

0.25

ClinPred

0.0092

GERP RS

-7.2

Varity_R

0.030

gMVP

0.17

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