rs17045761

chr1-207490011-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 0.0583 in 151,908 control chromosomes in the GnomAD database, including 317 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 0.058 (317 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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: 0.0584 AC: 8859 AN: 151786 Hom.: 318 Cov.: 32

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.0927

Gnomad FIN AF: 0.0675

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0501

Gnomad OTH AF: 0.0733

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.250 AC: 1 AN: 4 Hom.: 0 AF XY: 0.250 AC XY: 1 AN XY: 4

Gnomad4 AFR exome AF: 0.500

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.0583 AC: 8860 AN: 151908 Hom.: 317 Cov.: 32 AF XY: 0.0608 AC XY: 4509 AN XY: 74214

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.0665

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.0922

Gnomad4 FIN AF: 0.0675

Gnomad4 NFE AF: 0.0501

Gnomad4 OTH AF: 0.0743

Alfa AF: 0.0506 Hom.: 49

Bravo AF: 0.0581

Asia WGS AF: 0.0910 AC: 316 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.4
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17045761; hg19: chr1-207663356;