rs2180686

Variant names:

• chr20-6548823-T-C
• rs2180686

Your query was ambiguous. Multiple possible variants found:

• chr20-6548823-T-C
• chr20-6548823-T-G

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 0.822 in 151,380 control chromosomes in the GnomAD database, including 51,402 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 0.82 (51402 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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: 0.821 AC: 124241 AN: 151262 Hom.: 51337 Cov.: 30

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.768

Gnomad FIN AF: 0.762

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.822 AC: 124363 AN: 151380 Hom.: 51402 Cov.: 30 AF XY: 0.821 AC XY: 60682 AN XY: 73920

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.907

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.762

Gnomad4 NFE AF: 0.773

Gnomad4 OTH AF: 0.842

Alfa AF: 0.794 Hom.: 50468

Bravo AF: 0.834

Asia WGS AF: 0.845 AC: 2927 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.069
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2180686; hg19: chr20-6529470; COSMIC: COSV50253327;