rs1469557

Variant names:

• chr8-10849291-C-T
• rs1469557

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 0.179 in 152,102 control chromosomes in the GnomAD database, including 2,523 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 0.18 (2523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 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: 0.179 AC: 27218 AN: 151982 Hom.: 2519 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.179 AC: 27240 AN: 152102 Hom.: 2523 Cov.: 31 AF XY: 0.177 AC XY: 13126 AN XY: 74348

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.148

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.147

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.190

Alfa AF: 0.190 Hom.: 3630

Bravo AF: 0.175

Asia WGS AF: 0.145 AC: 503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469557; hg19: chr8-10706801;