rs1469170

Variant names:

• chr11-110870290-A-G
• rs1469170

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 0.547 in 151,986 control chromosomes in the GnomAD database, including 25,003 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 0.55 (25003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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: 0.547 AC: 83141 AN: 151868 Hom.: 24988 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.547 AC: 83184 AN: 151986 Hom.: 25003 Cov.: 32 AF XY: 0.544 AC XY: 40424 AN XY: 74264

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.600

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.589

Alfa AF: 0.642 Hom.: 30429

Bravo AF: 0.537

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.70
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1469170; hg19: chr11-110741014;