rs1576448

Variant names:

• chr20-6547561-A-G
• rs1576448

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 0.122 in 151,820 control chromosomes in the GnomAD database, including 1,288 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 0.12 (1288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 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: 0.122 AC: 18503 AN: 151700 Hom.: 1283 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.00757

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.122 AC: 18516 AN: 151820 Hom.: 1288 Cov.: 32 AF XY: 0.117 AC XY: 8714 AN XY: 74208

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.00740

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0448

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.148

Alfa AF: 0.113 Hom.: 142

Bravo AF: 0.127

Asia WGS AF: 0.0790 AC: 275 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1576448; hg19: chr20-6528208;