rs509356

Variant names:

• chr8-101488161-G-A
• rs509356
• ENST00000520268.1:n.50+4289C>T

Your query was ambiguous. Multiple possible variants found:

• chr8-101488161-G-A
• chr8-101488161-G-C
• chr8-101488161-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520268.1(GRHL2-DT):​n.50+4289C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.426 in 152,090 control chromosomes in the GnomAD database, including 15,222 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 0.43 (15222 hom., cov: 33)
• Consequence: GRHL2-DT ENST00000520268.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

Genes affected

GRHL2-DT (HGNC:):

GRHL2-DT (HGNC:55466): (GRHL2 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520268.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRHL2-DT	NR_186782.1		n.256+4289C>T		intron	N/A
	GRHL2-DT	NR_186785.1		n.58+4487C>T		intron	N/A
	GRHL2-DT	NR_186786.1		n.224+4168C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRHL2-DT	ENST00000520268.1	TSL:3	n.50+4289C>T		intron	N/A
	ENSG00000293625	ENST00000716497.1		n.172+4289C>T		intron	N/A
	GRHL2-DT	ENST00000716498.1		n.691+4487C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64697 AN: 151972 Hom.: 15196 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.311

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.426 AC: 64781 AN: 152090 Hom.: 15222 Cov.: 33 AF XY: 0.425 AC XY: 31568 AN XY: 74318

African (AFR) AF: 0.613 AC: 25439 AN: 41498

American (AMR) AF: 0.436 AC: 6662 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.311 AC: 1080 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3303 AN: 5178

South Asian (SAS) AF: 0.394 AC: 1898 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3331 AN: 10552

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21836 AN: 67978

Other (OTH) AF: 0.410 AC: 866 AN: 2114

Alfa AF: 0.345 Hom.: 5036

Bravo AF: 0.444

Asia WGS AF: 0.532 AC: 1849 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.1
DANN	Benign	0.49
PhyloP100		-0.21

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs509356;

hg19: chr8-102500389;