chr20-6340702-G-A

Position:

• chr20-6340702-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.299 in 152,020 control chromosomes in the GnomAD database, including 6,950 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 0.30 (6950 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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: 0.299 AC: 45447 AN: 151902 Hom.: 6949 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.410

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.299 AC: 45461 AN: 152020 Hom.: 6950 Cov.: 33 AF XY: 0.291 AC XY: 21650 AN XY: 74300

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.316

Gnomad4 OTH AF: 0.326

Alfa AF: 0.284 Hom.: 1068

Bravo AF: 0.298

Asia WGS AF: 0.190 AC: 660 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	19
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6085500; hg19: chr20-6321349;