rs6099314

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;