20-6785372-C-T

Variant names:

• chr20-6785372-C-T
• rs235757

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 0.716 in 152,078 control chromosomes in the GnomAD database, including 40,468 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 0.72 (40468 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.716 AC: 108728 AN: 151960 Hom.: 40408 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.716 AC: 108839 AN: 152078 Hom.: 40468 Cov.: 31 AF XY: 0.713 AC XY: 53016 AN XY: 74322

African (AFR) AF: 0.930 AC: 38624 AN: 41524

American (AMR) AF: 0.675 AC: 10319 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2589 AN: 3472

East Asian (EAS) AF: 0.608 AC: 3136 AN: 5158

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4818

European-Finnish (FIN) AF: 0.604 AC: 6374 AN: 10556

Middle Eastern (MID) AF: 0.772 AC: 227 AN: 294

European-Non Finnish (NFE) AF: 0.623 AC: 42361 AN: 67958

Other (OTH) AF: 0.735 AC: 1553 AN: 2112

Alfa AF: 0.648 Hom.: 39583

Bravo AF: 0.730

Asia WGS AF: 0.631 AC: 2198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.4
DANN	Benign	0.46
PhyloP100		0.067

Splicing

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

Other links and lift over

dbSNP: rs235757; hg19: chr20-6766019;