chr1-26583175-G-A

Variant names:

• chr1-26583175-G-A
• rs566421

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 0.331 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.176 AC: 7298 AN: 41500

American (AMR) AF: 0.341 AC: 5205 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3447 AN: 5172

South Asian (SAS) AF: 0.481 AC: 2319 AN: 4826

European-Finnish (FIN) AF: 0.364 AC: 3855 AN: 10590

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25396 AN: 67986

Other (OTH) AF: 0.376 AC: 795 AN: 2112

Alfa AF: 0.367 Hom.: 12735

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs566421; hg19: chr1-26909666;