rs6099314

Variant names:

• chr20-56879603-A-G
• rs6099314

Your query was ambiguous. Multiple possible variants found:

• chr20-56879603-A-G
• chr20-56879603-A-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 0.753 in 151,940 control chromosomes in the GnomAD database, including 44,954 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 (44954 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.874 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: 0.753 AC: 114320 AN: 151822 Hom.: 44946 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.763

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

GnomAD4 genome AF: 0.753 AC: 114362 AN: 151940 Hom.: 44954 Cov.: 31 AF XY: 0.754 AC XY: 55949 AN XY: 74240

African (AFR) AF: 0.519 AC: 21499 AN: 41396

American (AMR) AF: 0.714 AC: 10909 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2699 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3709 AN: 5154

South Asian (SAS) AF: 0.897 AC: 4319 AN: 4816

European-Finnish (FIN) AF: 0.842 AC: 8850 AN: 10506

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59846 AN: 68010

Other (OTH) AF: 0.764 AC: 1609 AN: 2106

Alfa AF: 0.838 Hom.: 36323

Bravo AF: 0.730

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.3
DANN	Benign	0.78
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs6099314; hg19: chr20-55454659;