rs9869409

Positions:

• chr3-180277213-G-A
• chr3-180277213-G-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 0.116 in 152,082 control chromosomes in the GnomAD database, including 1,398 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 0.12 (1398 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 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: 0.116 AC: 17609 AN: 151964 Hom.: 1396 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0783

Gnomad ASJ AF: 0.0755

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0505

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0687

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.116 AC: 17624 AN: 152082 Hom.: 1398 Cov.: 32 AF XY: 0.114 AC XY: 8485 AN XY: 74354

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0782

Gnomad4 ASJ AF: 0.0755

Gnomad4 EAS AF: 0.0178

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0505

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0818 Hom.: 383

Bravo AF: 0.121

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9869409; hg19: chr3-179995001;