Variant rs611419 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NR_186783.1(GRHL2-DT):n.1073A>T 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 0.25 in 152,172 control chromosomes in the GnomAD database, including 4,984 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 0.25 ( 4984 hom., cov: 33)

Consequence

GRHL2-DT
NR_186783.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.519

Variant links:

Genes affected

ENSG00000289048 (HGNC:):

ENSG00000289048 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
GRHL2-DT	NR_186783.1 linkuse as main transcript	n.1073A>T	non_coding_transcript_exon_variant	2/2
GRHL2-DT	NR_186784.1 linkuse as main transcript	n.691A>T	non_coding_transcript_exon_variant	3/3
GRHL2-DT	NR_186782.1 linkuse as main transcript	n.256+961A>T	intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
ENSG00000289048	ENST00000690034.1 linkuse as main transcript	n.621A>T	non_coding_transcript_exon_variant	2/2
ENSG00000289048	ENST00000701971.1 linkuse as main transcript	n.814A>T	non_coding_transcript_exon_variant	1/1
ENSG00000254024	ENST00000520268.1 linkuse as main transcript	n.50+961A>T	intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.250

AC:

37995

AN:

152054

Hom.:

4981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.212

Gnomad AMI

AF:

0.253

Gnomad AMR

AF:

0.313

Gnomad ASJ

AF:

0.195

Gnomad EAS

AF:

0.439

Gnomad SAS

AF:

0.291

Gnomad FIN

AF:

0.248

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.244

Gnomad OTH

AF:

0.252

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.250

AC:

38025

AN:

152172

Hom.:

4984

Cov.:

AF XY:

0.252

AC XY:

18722

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.212

Gnomad4 AMR

AF:

0.313

Gnomad4 ASJ

AF:

0.195

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.291

Gnomad4 FIN

AF:

0.248

Gnomad4 NFE

AF:

0.244

Gnomad4 OTH

AF:

0.257

Alfa

AF:

0.126

Hom.:

227

Bravo

AF:

0.252

Asia WGS

AF:

0.367

AC:

1274

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

DANN

Benign

0.80

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