20-6662560-T-C

Position:

• chr20-6662560-T-C

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 0.766 in 152,144 control chromosomes in the GnomAD database, including 44,828 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 0.77 (44828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 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: 0.766 AC: 116522 AN: 152026 Hom.: 44802 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.795

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.766 AC: 116596 AN: 152144 Hom.: 44828 Cov.: 32 AF XY: 0.762 AC XY: 56633 AN XY: 74362

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.795

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.764

Alfa AF: 0.776 Hom.: 32169

Bravo AF: 0.763

Asia WGS AF: 0.621 AC: 2160 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054434; hg19: chr20-6643207;