rs10955255

chr8-101524177-A-Gchr8-101524177-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024915.4(GRHL2):c.21-19064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 152,066 control chromosomes in the GnomAD database, including 17,570 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 0.45 (17570 hom., cov: 32)
• Consequence: GRHL2 NM_024915.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298

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 Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRHL2	NM_024915.4	c.21-19064A>G		intron_variant		ENST00000646743.1
GRHL2	NM_001330593.2	c.-28-19064A>G		intron_variant
GRHL2	XM_011517306.4	c.-28-19064A>G		intron_variant
GRHL2	XM_011517307.4	c.21-19064A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRHL2	ENST00000646743.1	c.21-19064A>G		intron_variant			NM_024915.4	P1
GRHL2	ENST00000472106.2	n.349-19064A>G		intron_variant, non_coding_transcript_variant		1
GRHL2	ENST00000395927.1	c.-28-19064A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68183 AN: 151948 Hom.: 17573 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.448 AC: 68196 AN: 152066 Hom.: 17570 Cov.: 32 AF XY: 0.448 AC XY: 33280 AN XY: 74346

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.293

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.450

Alfa AF: 0.538 Hom.: 29306

Bravo AF: 0.428

Asia WGS AF: 0.289 AC: 1010 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	1.1
Dann	Benign	0.87

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: rs10955255; hg19: chr8-102536405;