rs722589

Variant names:

• chr1-79708653-C-G
• rs722589

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 0.193 in 151,924 control chromosomes in the GnomAD database, including 3,764 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 0.19 (3764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.193 AC: 29293 AN: 151806 Hom.: 3768 Cov.: 32

Gnomad AFR AF: 0.0474

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.0270

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.193 AC: 29272 AN: 151924 Hom.: 3764 Cov.: 32 AF XY: 0.187 AC XY: 13857 AN XY: 74238

African (AFR) AF: 0.0473 AC: 1964 AN: 41516

American (AMR) AF: 0.239 AC: 3651 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1402 AN: 3468

East Asian (EAS) AF: 0.0275 AC: 142 AN: 5170

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4814

European-Finnish (FIN) AF: 0.137 AC: 1449 AN: 10586

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18700 AN: 67814

Other (OTH) AF: 0.243 AC: 512 AN: 2104

Alfa AF: 0.218 Hom.: 540

Bravo AF: 0.194

Asia WGS AF: 0.134 AC: 466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.48
DANN	Benign	0.47
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs722589; hg19: chr1-80174338;