20-7335335-G-C

Variant names:

• chr20-7335335-G-C
• rs6054926

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 0.571 in 151,674 control chromosomes in the GnomAD database, including 25,726 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 0.57 (25726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.999

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86434 AN: 151556 Hom.: 25685 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.571 AC: 86531 AN: 151674 Hom.: 25726 Cov.: 31 AF XY: 0.567 AC XY: 42004 AN XY: 74048

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.586

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.454

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.578

Alfa AF: 0.367 Hom.: 840

Bravo AF: 0.585

Asia WGS AF: 0.493 AC: 1711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6054926; hg19: chr20-7315982;