ENST00000598079.1:n.214-1230G>A

Variant names:

• chr19-50849681-G-A
• rs266868
• ENST00000598079.1:n.214-1230G>A

Variant summary

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

The ENST00000598079.1(ENSG00000267968):​n.214-1230G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,788 control chromosomes in the GnomAD database, including 8,512 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 0.33 (8512 hom., cov: 30)
• Consequence: ENSG00000267968 ENST00000598079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740
• Publications: 14 publications found

Genes affected

ENSG00000267968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372441	NR_131203.1	n.214-1230G>A		intron_variant	Intron 2 of 2
LOC105372441	NR_131205.1	n.231-1230G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267968	ENST00000598079.1	n.214-1230G>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50103 AN: 151670 Hom.: 8498 Cov.: 30

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.271

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.330 AC: 50153 AN: 151788 Hom.: 8512 Cov.: 30 AF XY: 0.333 AC XY: 24689 AN XY: 74168

African (AFR) AF: 0.402 AC: 16626 AN: 41354

American (AMR) AF: 0.238 AC: 3620 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5158

South Asian (SAS) AF: 0.336 AC: 1614 AN: 4810

European-Finnish (FIN) AF: 0.374 AC: 3934 AN: 10512

Middle Eastern (MID) AF: 0.277 AC: 81 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20508 AN: 67948

Other (OTH) AF: 0.314 AC: 659 AN: 2096

Alfa AF: 0.304 Hom.: 12020

Bravo AF: 0.323

Asia WGS AF: 0.364 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.49
PhyloP100		0.074

Splicing

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

Other links and lift over

dbSNP: rs266868; hg19: chr19-51352937;