Variant chr10-62666162-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The XM_047426120.1(LOC124902436):c.366C>A(p.Ile122=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000904 in 1,613,288 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 10 hom., cov: 32)

Exomes 𝑓: 0.00046 ( 8 hom. )

Consequence

LOC124902436
XM_047426120.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0630

Variant links:

Genes affected

LOC124902436 (HGNC:):

LOC124902436 links:

LINC02929 (HGNC:55812): (long intergenic non-protein coding RNA 2929)

LINC02929 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 10-62666162-C-A is Benign according to our data. Variant chr10-62666162-C-A is described in ClinVar as [Benign]. Clinvar id is 780866.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.063 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00517 (786/152164) while in subpopulation AFR AF= 0.0179 (742/41466). AF 95% confidence interval is 0.0168. There are 10 homozygotes in gnomad4. There are 386 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	Protein
LOC124902436	XM_047426120.1 linkuse as main transcript	c.366C>A	p.Ile122=	synonymous_variant	5/6	XP_047282076.1
LOC124902436	XM_047426121.1 linkuse as main transcript	c.672C>A	p.Ile224=	synonymous_variant	5/6	XP_047282077.1
LOC124902436	XM_047426118.1 linkuse as main transcript	c.522C>A	p.Ile174=	synonymous_variant	5/6	XP_047282074.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
LINC02929	ENST00000373784.6 linkuse as main transcript	n.404C>A	non_coding_transcript_exon_variant	4/5	1
LINC02929	ENST00000395249.5 linkuse as main transcript	n.225C>A	non_coding_transcript_exon_variant	2/3	1
LINC02929	ENST00000395251.5 linkuse as main transcript	n.850C>A	non_coding_transcript_exon_variant	6/7	1
LINC02929	ENST00000344640.7 linkuse as main transcript	n.371-4045C>A	intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.00514

AC:

781

AN:

152046

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0178

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.00122

AC:

306

AN:

251270

Hom.:

AF XY:

0.000935

AC XY:

127

AN XY:

135810

show subpopulations

Gnomad AFR exome

AF:

0.0172

Gnomad AMR exome

AF:

0.000579

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000440

Gnomad OTH exome

AF:

0.000326

GnomAD4 exome

AF:

0.000460

AC:

672

AN:

1461124

Hom.:

Cov.:

AF XY:

0.000421

AC XY:

306

AN XY:

726906

show subpopulations

Gnomad4 AFR exome

AF:

0.0169

Gnomad4 AMR exome

AF:

0.000761

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000144

Gnomad4 OTH exome

AF:

0.000895

GnomAD4 genome

AF:

0.00517

AC:

786

AN:

152164

Hom.:

Cov.:

AF XY:

0.00519

AC XY:

386

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0179

Gnomad4 AMR

AF:

0.00203

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00270

Hom.:

Bravo

AF:

0.00610

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0000546

EpiControl

AF:

0.0000593

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 09, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

3.8

DANN

Benign

0.40

Splicing

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