rs4810264

Variant names:

• chr20-39391934-C-G
• rs4810264
• ENST00000772859.1:n.459-9640C>G

Variant summary

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

The ENST00000772859.1(ENSG00000300599):​n.459-9640C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.327 in 151,998 control chromosomes in the GnomAD database, including 9,129 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 (9129 hom., cov: 32)
• Consequence: ENSG00000300599 ENST00000772859.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 1 publications found

Genes affected

ENSG00000300599 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 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
ENSG00000300599	ENST00000772859.1	n.459-9640C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49646 AN: 151880 Hom.: 9114 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.327 AC: 49670 AN: 151998 Hom.: 9129 Cov.: 32 AF XY: 0.332 AC XY: 24676 AN XY: 74272

African (AFR) AF: 0.184 AC: 7616 AN: 41470

American (AMR) AF: 0.496 AC: 7578 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2118 AN: 5168

South Asian (SAS) AF: 0.502 AC: 2409 AN: 4798

European-Finnish (FIN) AF: 0.345 AC: 3638 AN: 10560

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23593 AN: 67950

Other (OTH) AF: 0.344 AC: 725 AN: 2110

Alfa AF: 0.337 Hom.: 1165

Bravo AF: 0.332

Asia WGS AF: 0.480 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs4810264; hg19: chr20-38020577;