20-6682170-G-A

Position:

• chr20-6682170-G-A

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 0.0433 in 152,252 control chromosomes in the GnomAD database, including 329 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 0.043 (329 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0432 AC: 6566 AN: 152134 Hom.: 327 Cov.: 33

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.0204

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0449

Gnomad FIN AF: 0.00876

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00831

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0433 AC: 6591 AN: 152252 Hom.: 329 Cov.: 33 AF XY: 0.0426 AC XY: 3169 AN XY: 74446

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0204

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0451

Gnomad4 FIN AF: 0.00876

Gnomad4 NFE AF: 0.00831

Gnomad4 OTH AF: 0.0360

Alfa AF: 0.0309 Hom.: 34

Bravo AF: 0.0484

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.94
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1040568; hg19: chr20-6662817;