rs418919

chr9-99270227-A-Cchr9-99270227-A-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 0.62 in 152,016 control chromosomes in the GnomAD database, including 30,726 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 0.62 (30726 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94178 AN: 151898 Hom.: 30712 Cov.: 33

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.620 AC: 94225 AN: 152016 Hom.: 30726 Cov.: 33 AF XY: 0.627 AC XY: 46609 AN XY: 74288

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.703

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.775

Gnomad4 FIN AF: 0.753

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.608

Alfa AF: 0.552 Hom.: 1945

Bravo AF: 0.602

Asia WGS AF: 0.815 AC: 2832 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	9.1
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs418919; hg19: chr9-102032509; COSMIC: COSV60381276;