20-6792669-A-T

Variant names:

• chr20-6792669-A-T
• rs17804639

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0953 in 152,232 control chromosomes in the GnomAD database, including 815 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 0.095 (815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.539

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.127 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: 0.0953 AC: 14496 AN: 152114 Hom.: 812 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0869

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0953 AC: 14509 AN: 152232 Hom.: 815 Cov.: 32 AF XY: 0.0945 AC XY: 7031 AN XY: 74432

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0375

Gnomad4 FIN AF: 0.0729

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.0894

Alfa AF: 0.0432 Hom.: 35

Bravo AF: 0.104

Asia WGS AF: 0.0260 AC: 91 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17804639; hg19: chr20-6773316;