19-20866582-G-C

Variant names:

• chr19-20866582-G-C
• rs11085397
• ENST00000758057.1:n.407-1922C>G

Variant summary

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

The ENST00000758057.1(ENSG00000298806):​n.407-1922C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,082 control chromosomes in the GnomAD database, including 4,585 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 0.24 (4585 hom., cov: 32)
• Consequence: ENSG00000298806 ENST00000758057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.50
• Publications: 3 publications found

Genes affected

ENSG00000298806 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758057.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298806	ENST00000758057.1		n.407-1922C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36277 AN: 151964 Hom.: 4584 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.239 AC: 36288 AN: 152082 Hom.: 4585 Cov.: 32 AF XY: 0.234 AC XY: 17387 AN XY: 74348

African (AFR) AF: 0.271 AC: 11255 AN: 41480

American (AMR) AF: 0.179 AC: 2733 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3472

East Asian (EAS) AF: 0.157 AC: 813 AN: 5164

South Asian (SAS) AF: 0.185 AC: 895 AN: 4826

European-Finnish (FIN) AF: 0.187 AC: 1977 AN: 10580

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16540 AN: 67968

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.243 Hom.: 574

Bravo AF: 0.242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	8.5
DANN	Benign	0.69
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs11085397; hg19: chr19-21049388;