chr20-6868767-A-G

Position:

• chr20-6868767-A-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 0.024 in 152,378 control chromosomes in the GnomAD database, including 76 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 0.024 (76 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

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 (AMR) allele frequency at 95% confidence interval = 0.0546 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: 0.0239 AC: 3643 AN: 152260 Hom.: 75 Cov.: 33

Gnomad AFR AF: 0.00598

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0118

Gnomad FIN AF: 0.0304

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0304

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0240 AC: 3651 AN: 152378 Hom.: 76 Cov.: 33 AF XY: 0.0240 AC XY: 1788 AN XY: 74514

Gnomad4 AFR AF: 0.00596

Gnomad4 AMR AF: 0.0578

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0304

Gnomad4 NFE AF: 0.0304

Gnomad4 OTH AF: 0.0147

Alfa AF: 0.0272 Hom.: 13

Bravo AF: 0.0250

Asia WGS AF: 0.0110 AC: 38 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	1.3
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1500540; hg19: chr20-6849414;