20-7335335-G-C

Position:

• chr20-7335335-G-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 0.571 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;