chr20-6858477-C-T

Variant names:

• chr20-6858477-C-T
• rs1500537

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 0.591 in 151,946 control chromosomes in the GnomAD database, including 28,101 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 0.59 (28101 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.797 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: 0.591 AC: 89691 AN: 151824 Hom.: 28047 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.591 AC: 89811 AN: 151946 Hom.: 28101 Cov.: 31 AF XY: 0.588 AC XY: 43637 AN XY: 74258

African (AFR) AF: 0.804 AC: 33350 AN: 41462

American (AMR) AF: 0.553 AC: 8445 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1903 AN: 3472

East Asian (EAS) AF: 0.742 AC: 3826 AN: 5158

South Asian (SAS) AF: 0.530 AC: 2548 AN: 4806

European-Finnish (FIN) AF: 0.453 AC: 4769 AN: 10536

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33221 AN: 67930

Other (OTH) AF: 0.579 AC: 1222 AN: 2110

Alfa AF: 0.426 Hom.: 1335

Bravo AF: 0.609

Asia WGS AF: 0.651 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.7
DANN	Benign	0.45
PhyloP100		-0.030

Splicing

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

Other links and lift over

dbSNP: rs1500537; hg19: chr20-6839124;