Variant 12-80811600-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2

The NM_004664.4(LIN7A):c.567C>A(p.Thr189Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00981 in 1,613,904 control chromosomes in the GnomAD database, including 83 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0067 ( 7 hom., cov: 32)

Exomes 𝑓: 0.010 ( 76 hom. )

Consequence

LIN7A
NM_004664.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.162

Variant links:

Genes affected

LIN7A (HGNC:17787): (lin-7 homolog A, crumbs cell polarity complex component) The protein encoded by this gene is involved in generating and maintaining the asymmetric distribution of channels and receptors at the cell membrane. The encoded protein also is required for the localization of some specific channels and can be part of a protein complex that couples synaptic vesicle exocytosis to cell adhesion in the brain. [provided by RefSeq, May 2016]

LIN7A links:

LIN7A (HGNC:):

LIN7A links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.43).

BP6

Variant 12-80811600-G-T is Benign according to our data. Variant chr12-80811600-G-T is described in ClinVar as [Benign]. Clinvar id is 782781.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LIN7A	NM_004664.4 linkuse as main transcript	c.567C>A	p.Thr189Thr	synonymous_variant	5/6	ENST00000552864.6	NP_004655.1	O14910

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
LIN7A	ENST00000552864.6 linkuse as main transcript	c.567C>A	p.Thr189Thr	synonymous_variant	5/6	1	NM_004664.4	ENSP00000447488.1	O14910
LIN7A	ENST00000261203.7 linkuse as main transcript	n.*338C>A		non_coding_transcript_exon_variant	6/7	1		ENSP00000261203.3	J3KN23
LIN7A	ENST00000261203.7 linkuse as main transcript	n.*338C>A		3_prime_UTR_variant	6/7	1		ENSP00000261203.3	J3KN23

Frequencies

GnomAD3 genomes

AF:

0.00668

AC:

1015

AN:

151944

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00196

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.00243

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00395

Gnomad FIN

AF:

0.0149

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.00432

GnomAD3 exomes

AF:

0.00802

AC:

2016

AN:

251402

Hom.:

AF XY:

0.00794

AC XY:

1079

AN XY:

135868

show subpopulations

Gnomad AFR exome

AF:

0.00221

Gnomad AMR exome

AF:

0.00376

Gnomad ASJ exome

AF:

0.0000992

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00611

Gnomad FIN exome

AF:

0.0175

Gnomad NFE exome

AF:

0.0108

Gnomad OTH exome

AF:

0.00880

GnomAD4 exome

AF:

0.0101

AC:

14821

AN:

1461842

Hom.:

Cov.:

AF XY:

0.00995

AC XY:

7236

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.00134

Gnomad4 AMR exome

AF:

0.00387

Gnomad4 ASJ exome

AF:

0.000230

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00604

Gnomad4 FIN exome

AF:

0.0158

Gnomad4 NFE exome

AF:

0.0115

Gnomad4 OTH exome

AF:

0.00765

GnomAD4 genome

AF:

0.00667

AC:

1014

AN:

152062

Hom.:

Cov.:

AF XY:

0.00628

AC XY:

467

AN XY:

74350

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00236

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00395

Gnomad4 FIN

AF:

0.0149

Gnomad4 NFE

AF:

0.0104

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00802

Hom.:

Bravo

AF:

0.00589

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0105

EpiControl

AF:

0.00972

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.43

CADD

Benign

7.5

DANN

Benign

0.67

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