20-7658056-A-G

Position:

• chr20-7658056-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 0.268 in 150,636 control chromosomes in the GnomAD database, including 6,133 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 0.27 (6133 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.379 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: 0.268 AC: 40408 AN: 150526 Hom.: 6128 Cov.: 31

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.268 AC: 40421 AN: 150636 Hom.: 6133 Cov.: 31 AF XY: 0.267 AC XY: 19697 AN XY: 73660

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.257

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.307

Alfa AF: 0.312 Hom.: 13072

Bravo AF: 0.274

Asia WGS AF: 0.286 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6086149; hg19: chr20-7638703;