chr19-20663465-C-G

Variant names:

• chr19-20663465-C-G
• rs4808260
• ENST00000805334.1:n.71+434C>G

Variant summary

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

The ENST00000805334.1(ENSG00000304675):​n.71+434C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 151,796 control chromosomes in the GnomAD database, including 39,120 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 0.71 (39120 hom., cov: 30)
• Consequence: ENSG00000304675 ENST00000805334.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.869
• Publications: 11 publications found

Genes affected

ENSG00000304675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805334.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304675	ENST00000805334.1		n.71+434C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108453 AN: 151680 Hom.: 39094 Cov.: 30

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.656

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.715 AC: 108524 AN: 151796 Hom.: 39120 Cov.: 30 AF XY: 0.715 AC XY: 53020 AN XY: 74130

African (AFR) AF: 0.672 AC: 27786 AN: 41318

American (AMR) AF: 0.656 AC: 10002 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2703 AN: 3468

East Asian (EAS) AF: 0.584 AC: 2999 AN: 5132

South Asian (SAS) AF: 0.683 AC: 3291 AN: 4818

European-Finnish (FIN) AF: 0.796 AC: 8394 AN: 10540

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50824 AN: 67962

Other (OTH) AF: 0.723 AC: 1528 AN: 2112

Alfa AF: 0.734 Hom.: 5110

Bravo AF: 0.701

Asia WGS AF: 0.628 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.18
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs4808260; hg19: chr19-20846271;