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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.753 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

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.897

Gnomad4 FIN AF: 0.842

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.764

Alfa AF: 0.852 Hom.: 25103

Bravo AF: 0.730

Asia WGS AF: 0.764 AC: 2656 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6099314; hg19: chr20-55454659;