20-6787030-C-G

Variant names:

• chr20-6787030-C-G
• rs235754

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 0.492 in 151,964 control chromosomes in the GnomAD database, including 18,808 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 0.49 (18808 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.702
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.505 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: 0.492 AC: 74686 AN: 151846 Hom.: 18799 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.492 AC: 74718 AN: 151964 Hom.: 18808 Cov.: 32 AF XY: 0.493 AC XY: 36591 AN XY: 74272

African (AFR) AF: 0.477 AC: 19755 AN: 41434

American (AMR) AF: 0.504 AC: 7703 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2003 AN: 3472

East Asian (EAS) AF: 0.153 AC: 789 AN: 5168

South Asian (SAS) AF: 0.484 AC: 2334 AN: 4818

European-Finnish (FIN) AF: 0.546 AC: 5763 AN: 10552

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34646 AN: 67938

Other (OTH) AF: 0.520 AC: 1099 AN: 2112

Alfa AF: 0.359 Hom.: 953

Bravo AF: 0.487

Asia WGS AF: 0.331 AC: 1151 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	8.2
DANN	Benign	0.74
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs235754; hg19: chr20-6767677;