rs418919

Variant names:

• chr9-99270227-A-C
• rs418919

Your query was ambiguous. Multiple possible variants found:

• chr9-99270227-A-C
• chr9-99270227-A-T

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 0.62 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.414 AC: 17181 AN: 41456

American (AMR) AF: 0.636 AC: 9716 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2439 AN: 3468

East Asian (EAS) AF: 0.892 AC: 4623 AN: 5182

South Asian (SAS) AF: 0.775 AC: 3737 AN: 4820

European-Finnish (FIN) AF: 0.753 AC: 7926 AN: 10522

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.686 AC: 46655 AN: 67968

Other (OTH) AF: 0.608 AC: 1285 AN: 2112

Alfa AF: 0.543 Hom.: 2020

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
PhyloP100		1.6

Splicing

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

Other links and lift over

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