rs6670533

Variant summary

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

The ENST00000690803.1(GRHL3):​c.-76+21163G>A variant causes a intron change. The variant allele was found at a frequency of 0.0872 in 152,286 control chromosomes in the GnomAD database, including 643 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 0.087 ( 643 hom., cov: 32)

Consequence

GRHL3
ENST00000690803.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.29
Variant links:
Genes affected
GRHL3 (HGNC:25839): (grainyhead like transcription factor 3) This gene encodes a member of the grainyhead family of transcription factors. The encoded protein may function as a transcription factor during development, and has been shown to stimulate migration of endothelial cells. Multiple transcript variants encoding distinct isoforms have been identified for this gene.[provided by RefSeq, Aug 2010]

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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=-0.73).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GRHL3ENST00000690803.1 linkc.-76+21163G>A intron_variant Intron 2 of 15 ENSP00000510783.1 Q8TE85-4

Frequencies

GnomAD3 genomes
AF:
0.0871
AC:
13247
AN:
152168
Hom.:
638
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.123
Gnomad AMI
AF:
0.0965
Gnomad AMR
AF:
0.0648
Gnomad ASJ
AF:
0.0908
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.0474
Gnomad FIN
AF:
0.0902
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.0779
Gnomad OTH
AF:
0.0999
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0872
AC:
13273
AN:
152286
Hom.:
643
Cov.:
32
AF XY:
0.0850
AC XY:
6332
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.124
Gnomad4 AMR
AF:
0.0647
Gnomad4 ASJ
AF:
0.0908
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.0476
Gnomad4 FIN
AF:
0.0902
Gnomad4 NFE
AF:
0.0779
Gnomad4 OTH
AF:
0.0989
Alfa
AF:
0.0741
Hom.:
561
Bravo
AF:
0.0861
Asia WGS
AF:
0.0310
AC:
111
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.73
CADD
Benign
13
DANN
Benign
0.41

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.

Other links and lift over

dbSNP: rs6670533; hg19: chr1-24584490; API