Variant 3-15175196-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000446690.2(COL6A4P1):n.1008T>A variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.184 in 459,080 control chromosomes in the GnomAD database, including 9,516 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2405 hom., cov: 32)

Exomes 𝑓: 0.20 ( 7111 hom. )

Consequence

COL6A4P1
ENST00000446690.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.81

Variant links:

Genes affected

COL6A4P1 (HGNC:):

COL6A4P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL6A4P1	NR_027927.1 linkuse as main transcript	n.1008T>A		non_coding_transcript_exon_variant	3/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL6A4P1	ENST00000446690.2 linkuse as main transcript	n.1008T>A		non_coding_transcript_exon_variant	3/5	2
COL6A4P1	ENST00000487147.5 linkuse as main transcript	n.832T>A		non_coding_transcript_exon_variant	3/13	6

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

24068

AN:

152002

Hom.:

2394

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0987

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.0836

Gnomad EAS

AF:

0.490

Gnomad SAS

AF:

0.315

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.159

GnomAD3 exomes

AF:

0.210

AC:

28809

AN:

136950

Hom.:

3836

AF XY:

0.214

AC XY:

15898

AN XY:

74360

show subpopulations

Gnomad AFR exome

AF:

0.0941

Gnomad AMR exome

AF:

0.225

Gnomad ASJ exome

AF:

0.0766

Gnomad EAS exome

AF:

0.497

Gnomad SAS exome

AF:

0.297

Gnomad FIN exome

AF:

0.138

Gnomad NFE exome

AF:

0.158

Gnomad OTH exome

AF:

0.170

GnomAD4 exome

AF:

0.196

AC:

60220

AN:

306960

Hom.:

7111

Cov.:

AF XY:

0.206

AC XY:

36001

AN XY:

174728

show subpopulations

Gnomad4 AFR exome

AF:

0.0953

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.0783

Gnomad4 EAS exome

AF:

0.485

Gnomad4 SAS exome

AF:

0.292

Gnomad4 FIN exome

AF:

0.139

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.183

GnomAD4 genome

AF:

0.158

AC:

24104

AN:

152120

Hom.:

2405

Cov.:

AF XY:

0.163

AC XY:

12142

AN XY:

74344

show subpopulations

Gnomad4 AFR

AF:

0.0987

Gnomad4 AMR

AF:

0.194

Gnomad4 ASJ

AF:

0.0836

Gnomad4 EAS

AF:

0.490

Gnomad4 SAS

AF:

0.317

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.168

Alfa

AF:

0.0974

Hom.:

205

Bravo

AF:

0.159

Asia WGS

AF:

0.393

AC:

1366

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

DANN

Benign

0.70

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over