rs566421

Variant names:

• chr1-26583175-G-A
• rs566421

Your query was ambiguous. Multiple possible variants found:

• chr1-26583175-G-A
• chr1-26583175-G-C
• chr1-26583175-G-T

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 0.331 in 152,134 control chromosomes in the GnomAD database, including 9,295 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 0.33 (9295 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.648 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: 0.331 AC: 50294 AN: 152016 Hom.: 9296 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.331 AC: 50310 AN: 152134 Hom.: 9295 Cov.: 32 AF XY: 0.335 AC XY: 24906 AN XY: 74386

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.376

Alfa AF: 0.379 Hom.: 7940

Bravo AF: 0.321

Asia WGS AF: 0.544 AC: 1889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs566421; hg19: chr1-26909666;