chr1-24336215-G-GT

Position:

• chr1-24336215-G-GT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_198173.3(GRHL3):​c.267-253dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.019 in 142,228 control chromosomes in the GnomAD database, including 57 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.019 (57 hom., cov: 31)
• Consequence: GRHL3 NM_198173.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.784

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-24336215-G-GT is Benign according to our data. Variant chr1-24336215-G-GT is described in ClinVar as [Benign]. Clinvar id is 1295139.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRHL3	NM_198173.3	c.267-253dup		intron_variant		ENST00000361548.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRHL3	ENST00000361548.9	c.267-253dup		intron_variant		1	NM_198173.3	P1

Frequencies

GnomAD3 genomes AF: 0.0189 AC: 2685 AN: 142204 Hom.: 57 Cov.: 31

Gnomad AFR AF: 0.0518

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00908

Gnomad ASJ AF: 0.0108

Gnomad EAS AF: 0.00122

Gnomad SAS AF: 0.0131

Gnomad FIN AF: 0.00853

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00501

Gnomad OTH AF: 0.0201

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

GnomAD4 genome AF: 0.0190 AC: 2708 AN: 142228 Hom.: 57 Cov.: 31 AF XY: 0.0189 AC XY: 1301 AN XY: 69008

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.00907

Gnomad4 ASJ AF: 0.0108

Gnomad4 EAS AF: 0.00122

Gnomad4 SAS AF: 0.0131

Gnomad4 FIN AF: 0.00853

Gnomad4 NFE AF: 0.00502

Gnomad4 OTH AF: 0.0204

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 21, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs57566921; hg19: chr1-24662705;