Variant rs1771889 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000637541.1(ENSG00000227355):n.112A>G 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 0.403 in 188,048 control chromosomes in the GnomAD database, including 16,215 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 0.41 ( 13595 hom., cov: 33)

Exomes 𝑓: 0.36 ( 2620 hom. )

Consequence

ENSG00000227355
ENST00000637541.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.424

Variant links:

Genes affected

ENSG00000227355 (HGNC:):

ENSG00000227355 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
LOC102723324	NR_187150.1 linkuse as main transcript	n.88A>G	non_coding_transcript_exon_variant	1/3
LOC102723324	NR_187151.1 linkuse as main transcript	n.88A>G	non_coding_transcript_exon_variant	1/3
LOC102723324	NR_187152.1 linkuse as main transcript	n.88A>G	non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000227355	ENST00000637541.1 linkuse as main transcript	n.112A>G	non_coding_transcript_exon_variant	1/3	3
ENSG00000227355	ENST00000685727.1 linkuse as main transcript	n.55A>G	non_coding_transcript_exon_variant	1/4
ENSG00000227355	ENST00000688457.1 linkuse as main transcript	n.9A>G	non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes

AF:

0.413

AC:

62699

AN:

151990

Hom.:

13561

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.541

Gnomad AMR

AF:

0.333

Gnomad ASJ

AF:

0.499

Gnomad EAS

AF:

0.127

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.407

GnomAD4 exome

AF:

0.360

AC:

12929

AN:

35940

Hom.:

2620

Cov.:

AF XY:

0.350

AC XY:

6688

AN XY:

19108

show subpopulations

Gnomad4 AFR exome

AF:

0.508

Gnomad4 AMR exome

AF:

0.248

Gnomad4 ASJ exome

AF:

0.494

Gnomad4 EAS exome

AF:

0.102

Gnomad4 SAS exome

AF:

0.211

Gnomad4 FIN exome

AF:

0.325

Gnomad4 NFE exome

AF:

0.404

Gnomad4 OTH exome

AF:

0.399

GnomAD4 genome

AF:

0.413

AC:

62779

AN:

152108

Hom.:

13595

Cov.:

AF XY:

0.404

AC XY:

30032

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.333

Gnomad4 ASJ

AF:

0.499

Gnomad4 EAS

AF:

0.128

Gnomad4 SAS

AF:

0.225

Gnomad4 FIN

AF:

0.345

Gnomad4 NFE

AF:

0.417

Gnomad4 OTH

AF:

0.403

Alfa

AF:

0.416

Hom.:

2776

Bravo

AF:

0.417

Asia WGS

AF:

0.199

AC:

694

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.4

DANN

Benign

0.65

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