rs1569475

Positions:

• chr1-169654442-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;