chr20-6707758-C-T

Variant names:

• chr20-6707758-C-T
• rs727689

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 0.586 in 152,074 control chromosomes in the GnomAD database, including 27,003 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 (27003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 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: 0.586 AC: 89112 AN: 151956 Hom.: 26994 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.586 AC: 89138 AN: 152074 Hom.: 27003 Cov.: 32 AF XY: 0.589 AC XY: 43774 AN XY: 74330

African (AFR) AF: 0.416 AC: 17262 AN: 41464

American (AMR) AF: 0.635 AC: 9692 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2227 AN: 3470

East Asian (EAS) AF: 0.556 AC: 2874 AN: 5166

South Asian (SAS) AF: 0.558 AC: 2686 AN: 4810

European-Finnish (FIN) AF: 0.700 AC: 7413 AN: 10584

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44863 AN: 67988

Other (OTH) AF: 0.594 AC: 1255 AN: 2112

Alfa AF: 0.636 Hom.: 54652

Bravo AF: 0.578

Asia WGS AF: 0.511 AC: 1779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.55
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs727689; hg19: chr20-6688405;