8-101543240-G-A

Variant names:

• chr8-101543240-G-A
• NM_024915.4:c.21-1G>A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_024915.4(GRHL2):​c.21-1G>A variant causes a splice acceptor, intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GRHL2 NM_024915.4 splice_acceptor, intron
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 6.85

Genes affected

GRHL2 (HGNC:2799): (grainyhead like transcription factor 2) The protein encoded by this gene is a transcription factor that can act as a homodimer or as a heterodimer with either GRHL1 or GRHL3. Defects in this gene are a cause of non-syndromic sensorineural deafness autosomal dominant type 28 (DFNA28).[provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 8-101543240-G-A is Pathogenic according to our data. Variant chr8-101543240-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2635445.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRHL2	NM_024915.4	c.21-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15	ENST00000646743.1	NP_079191.2
GRHL2	NM_001330593.2	c.-28-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15		NP_001317522.1
GRHL2	XM_011517306.4	c.-28-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15		XP_011515608.1
GRHL2	XM_011517307.4	c.21-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15		XP_011515609.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRHL2	ENST00000646743.1	c.21-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15		NM_024915.4	ENSP00000495564.1
GRHL2	ENST00000472106.2	n.349-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 1	1
GRHL2	ENST00000395927.1	c.-28-1G>A		splice_acceptor_variant, intron_variant	Intron 1 of 15	2		ENSP00000379260.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

EpiCase AF: 0.0000545

EpiControl AF: 0.00

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

GRHL2-related disorder Pathogenic:1

Dec 11, 2022

PreventionGenetics, part of Exact Sciences

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The GRHL2 c.21-1G>A variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. A different variant affecting the same consensus splice site, c.21-2A>G, is reported in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/1324514). Variants that disrupt the consensus splice acceptor site in GRHL2 are expected to be pathogenic. The c.21-1G>A variant is interpreted as likely pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.22
CADD	Pathogenic	36
DANN	Uncertain	0.99
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.76
FATHMM_MKL	Uncertain	0.95	D
ClinPred		0.99	D
GERP RS		6.0

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.94
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.96		Position offset: 10
DS_AL_spliceai		1.0		Position offset: 1

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-102555468;