rs611419

Variant names:

• chr8-101491489-T-A
• rs611419
• ENST00000690034.2:n.694A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-101491489-T-A
• chr8-101491489-T-C
• chr8-101491489-T-G

Variant summary

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

The ENST00000690034.2(GRHL2-DT):​n.694A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,172 control chromosomes in the GnomAD database, including 4,984 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 0.25 (4984 hom., cov: 33)
• Consequence: GRHL2-DT ENST00000690034.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 9 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=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRHL2-DT	NR_186783.1	n.1073A>T		non_coding_transcript_exon_variant	Exon 2 of 2
GRHL2-DT	NR_186784.1	n.691A>T		non_coding_transcript_exon_variant	Exon 3 of 3
GRHL2-DT	NR_186782.1	n.256+961A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRHL2-DT	ENST00000690034.2	n.694A>T		non_coding_transcript_exon_variant	Exon 3 of 3
GRHL2-DT	ENST00000701971.2	n.1246A>T		non_coding_transcript_exon_variant	Exon 2 of 2
GRHL2-DT	ENST00000716503.1	n.398A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37995 AN: 152054 Hom.: 4981 Cov.: 33

Gnomad AFR AF: 0.212

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.250 AC: 38025 AN: 152172 Hom.: 4984 Cov.: 33 AF XY: 0.252 AC XY: 18722 AN XY: 74404

African (AFR) AF: 0.212 AC: 8786 AN: 41532

American (AMR) AF: 0.313 AC: 4782 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2271 AN: 5166

South Asian (SAS) AF: 0.291 AC: 1403 AN: 4816

European-Finnish (FIN) AF: 0.248 AC: 2626 AN: 10592

Middle Eastern (MID) AF: 0.308 AC: 90 AN: 292

European-Non Finnish (NFE) AF: 0.244 AC: 16620 AN: 68008

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.126 Hom.: 227

Bravo AF: 0.252

Asia WGS AF: 0.367 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.80
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs611419; hg19: chr8-102503717;