rs17654531

Variant names:

• chr1-111257063-A-G
• rs17654531

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 0.0832 in 152,230 control chromosomes in the GnomAD database, including 661 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 0.083 (661 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.11 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: 0.0832 AC: 12653 AN: 152112 Hom.: 661 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.00752

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0656

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

GnomAD4 genome AF: 0.0832 AC: 12661 AN: 152230 Hom.: 661 Cov.: 32 AF XY: 0.0851 AC XY: 6336 AN XY: 74436

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.0529

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.00773

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.103 Hom.: 465

Bravo AF: 0.0694

Asia WGS AF: 0.0600 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17654531; hg19: chr1-111799685;