20-7335335-G-C

Variant names:

• chr20-7335335-G-C
• rs6054926

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.741 AC: 30703 AN: 41412

American (AMR) AF: 0.586 AC: 8905 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1960 AN: 3466

East Asian (EAS) AF: 0.392 AC: 2012 AN: 5136

South Asian (SAS) AF: 0.490 AC: 2346 AN: 4790

European-Finnish (FIN) AF: 0.454 AC: 4777 AN: 10514

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.501 AC: 33980 AN: 67852

Other (OTH) AF: 0.578 AC: 1213 AN: 2098

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6054926; hg19: chr20-7315982;