rs722589

chr1-79708653-C-G

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 0.193 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0473

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.404

Gnomad4 EAS AF: 0.0275

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.243

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs722589; hg19: chr1-80174338;