dbSNP rs13273073: ENSG00000254002:n.231C>A (chr8-23726713-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000686210.1(ENSG00000254002):n.231C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,210 control chromosomes in the GnomAD database, including 4,830 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 0.24 ( 4828 hom., cov: 32)

Exomes 𝑓: 0.21 ( 2 hom. )

Consequence

ENSG00000254002
ENST00000686210.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.197

Variant links:

Genes affected

ENSG00000254002 (HGNC:):

ENSG00000254002 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=-0.79).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101929258	NR_188036.1 link	n.94-102C>A	intron_variant	Intron 1 of 3
LOC101929258	NR_188037.1 link	n.94-102C>A	intron_variant	Intron 1 of 3
LOC101929258	NR_188038.1 link	n.94-102C>A	intron_variant	Intron 1 of 3
LOC107986930	XR_001745842.2 link	n.1312+57963G>T	intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000254002	ENST00000686210.1 link	n.231C>A	non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000254002	ENST00000702219.1 link	n.123C>A	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000254002	ENST00000520375.1 link	n.163-102C>A	intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.245

AC:

37215

AN:

152000

Hom.:

4824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.288

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.299

Gnomad EAS

AF:

0.0820

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.211

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.264

GnomAD4 exome

AF:

0.207

AC:

AN:

Hom.:

AF XY:

0.197

AC XY:

AN XY:

show subpopulations

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.375

Gnomad4 NFE exome

AF:

0.191

Gnomad4 OTH exome

AF:

0.167

GnomAD4 genome

AF:

0.245

AC:

37254

AN:

152118

Hom.:

4828

Cov.:

AF XY:

0.242

AC XY:

18007

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.189

Gnomad4 ASJ

AF:

0.299

Gnomad4 EAS

AF:

0.0822

Gnomad4 SAS

AF:

0.337

Gnomad4 FIN

AF:

0.211

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.265

Alfa

AF:

0.244

Hom.:

9228

Bravo

AF:

0.243

Asia WGS

AF:

0.264

AC:

916

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.6

DANN

Benign

0.88

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