rs1569475

Variant names:

• chr1-169654442-C-T
• rs1569475

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.165 AC: 6841 AN: 41480

American (AMR) AF: 0.0755 AC: 1155 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0196 AC: 68 AN: 3470

East Asian (EAS) AF: 0.00869 AC: 45 AN: 5178

South Asian (SAS) AF: 0.0932 AC: 449 AN: 4818

European-Finnish (FIN) AF: 0.0894 AC: 947 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0544 AC: 3699 AN: 68010

Other (OTH) AF: 0.0658 AC: 139 AN: 2112

Alfa AF: 0.0627 Hom.: 1573

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
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs1569475; hg19: chr1-169623680;