rs4808564

Variant names:

• chr19-14853283-C-A
• rs4808564
• ENST00000816598.1:n.190-326G>T

Variant summary

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

The ENST00000816598.1(ENSG00000306269):​n.190-326G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0651 in 152,118 control chromosomes in the GnomAD database, including 372 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 0.065 (372 hom., cov: 32)
• Consequence: ENSG00000306269 ENST00000816598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 3 publications found

Genes affected

ENSG00000306269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306269	ENST00000816598.1	n.190-326G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0652 AC: 9903 AN: 152000 Hom.: 373 Cov.: 32

Gnomad AFR AF: 0.0684

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.0403

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0620

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0651 AC: 9900 AN: 152118 Hom.: 372 Cov.: 32 AF XY: 0.0662 AC XY: 4922 AN XY: 74366

African (AFR) AF: 0.0683 AC: 2832 AN: 41494

American (AMR) AF: 0.0640 AC: 979 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3466

East Asian (EAS) AF: 0.106 AC: 551 AN: 5186

South Asian (SAS) AF: 0.125 AC: 602 AN: 4818

European-Finnish (FIN) AF: 0.0403 AC: 427 AN: 10588

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0620 AC: 4212 AN: 67960

Other (OTH) AF: 0.0672 AC: 142 AN: 2114

Alfa AF: 0.0622 Hom.: 406

Bravo AF: 0.0650

Asia WGS AF: 0.109 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4808564; hg19: chr19-14964095;