rs17423694

chr1-87482840-G-A

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 0.0635 in 151,896 control chromosomes in the GnomAD database, including 353 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 0.063 (353 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0807 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: 0.0635 AC: 9639 AN: 151778 Hom.: 353 Cov.: 33

Gnomad AFR AF: 0.0392

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.0602

Gnomad ASJ AF: 0.0815

Gnomad EAS AF: 0.00579

Gnomad SAS AF: 0.0403

Gnomad FIN AF: 0.0715

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0825

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0635 AC: 9641 AN: 151896 Hom.: 353 Cov.: 33 AF XY: 0.0612 AC XY: 4540 AN XY: 74206

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0601

Gnomad4 ASJ AF: 0.0815

Gnomad4 EAS AF: 0.00581

Gnomad4 SAS AF: 0.0401

Gnomad4 FIN AF: 0.0715

Gnomad4 NFE AF: 0.0825

Gnomad4 OTH AF: 0.0682

Alfa AF: 0.0644 Hom.: 58

Bravo AF: 0.0619

Asia WGS AF: 0.0350 AC: 122 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.87
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17423694; hg19: chr1-87948523;