rs1774886

Positions:

• chr20-6147576-G-A
• chr20-6147576-G-C

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 0.813 in 152,118 control chromosomes in the GnomAD database, including 50,359 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 0.81 (50359 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123617 AN: 152000 Hom.: 50313 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.883

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.813 AC: 123721 AN: 152118 Hom.: 50359 Cov.: 32 AF XY: 0.812 AC XY: 60338 AN XY: 74350

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.794

Gnomad4 FIN AF: 0.772

Gnomad4 NFE AF: 0.824

Gnomad4 OTH AF: 0.800

Alfa AF: 0.823 Hom.: 63887

Bravo AF: 0.818

Asia WGS AF: 0.862 AC: 2996 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1774886; hg19: chr20-6128223;