rs10020466

Variant names:

• chr4-180385494-G-A
• rs10020466

Variant summary

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

The variant allele was found at a frequency of 0.752 in 152,050 control chromosomes in the GnomAD database, including 43,134 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 0.75 (43134 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.227
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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

Frequencies

GnomAD3 genomes AF: 0.752 AC: 114224 AN: 151932 Hom.: 43095 Cov.: 31

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.752 AC: 114317 AN: 152050 Hom.: 43134 Cov.: 31 AF XY: 0.756 AC XY: 56167 AN XY: 74330

African (AFR) AF: 0.761 AC: 31553 AN: 41480

American (AMR) AF: 0.770 AC: 11757 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2349 AN: 3466

East Asian (EAS) AF: 0.891 AC: 4598 AN: 5162

South Asian (SAS) AF: 0.823 AC: 3970 AN: 4824

European-Finnish (FIN) AF: 0.788 AC: 8328 AN: 10562

Middle Eastern (MID) AF: 0.724 AC: 210 AN: 290

European-Non Finnish (NFE) AF: 0.729 AC: 49531 AN: 67966

Other (OTH) AF: 0.733 AC: 1548 AN: 2112

Alfa AF: 0.734 Hom.: 53613

Bravo AF: 0.749

Asia WGS AF: 0.812 AC: 2824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.52
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10020466; hg19: chr4-181306647;