rs1884917

Variant names:

• chr20-4595423-C-G
• rs1884917

Your query was ambiguous. Multiple possible variants found:

• chr20-4595423-C-G
• chr20-4595423-C-T

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 0.681 in 152,070 control chromosomes in the GnomAD database, including 36,066 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 0.68 (36066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 1 publications found

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 = 0.759 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103428 AN: 151952 Hom.: 36049 Cov.: 31

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.806

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.681 AC: 103485 AN: 152070 Hom.: 36066 Cov.: 31 AF XY: 0.678 AC XY: 50424 AN XY: 74356

African (AFR) AF: 0.564 AC: 23368 AN: 41438

American (AMR) AF: 0.651 AC: 9947 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2206 AN: 5172

South Asian (SAS) AF: 0.608 AC: 2934 AN: 4822

European-Finnish (FIN) AF: 0.806 AC: 8530 AN: 10586

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51978 AN: 67988

Other (OTH) AF: 0.673 AC: 1421 AN: 2110

Alfa AF: 0.718 Hom.: 4691

Bravo AF: 0.664

Asia WGS AF: 0.523 AC: 1817 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	0.14
DANN	Benign	0.57
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1884917; hg19: chr20-4576069;