chr20-6357333-C-T

Variant names:

• chr20-6357333-C-T
• rs6038449

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 0.708 in 152,096 control chromosomes in the GnomAD database, including 38,880 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 0.71 (38880 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 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: 0.708 AC: 107537 AN: 151978 Hom.: 38840 Cov.: 33

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.708 AC: 107638 AN: 152096 Hom.: 38880 Cov.: 33 AF XY: 0.707 AC XY: 52566 AN XY: 74364

African (AFR) AF: 0.833 AC: 34574 AN: 41504

American (AMR) AF: 0.737 AC: 11277 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2649 AN: 3472

East Asian (EAS) AF: 0.883 AC: 4572 AN: 5178

South Asian (SAS) AF: 0.603 AC: 2903 AN: 4818

European-Finnish (FIN) AF: 0.659 AC: 6953 AN: 10554

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42437 AN: 67964

Other (OTH) AF: 0.748 AC: 1576 AN: 2106

Alfa AF: 0.656 Hom.: 31168

Bravo AF: 0.726

Asia WGS AF: 0.738 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.059
DANN	Benign	0.75
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs6038449; hg19: chr20-6337980;