rs1569475

Variant names:

• chr1-169654442-C-T
• rs1569475

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 0.0884 in 152,164 control chromosomes in the GnomAD database, including 782 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 0.088 (782 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.84

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 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: 0.0884 AC: 13437 AN: 152046 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0754

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.0894

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0884 AC: 13450 AN: 152164 Hom.: 782 Cov.: 32 AF XY: 0.0892 AC XY: 6635 AN XY: 74398

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.00869

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.0894

Gnomad4 NFE AF: 0.0544

Gnomad4 OTH AF: 0.0658

Alfa AF: 0.0567 Hom.: 579

Bravo AF: 0.0897

Asia WGS AF: 0.0630 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.026
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1569475; hg19: chr1-169623680;