rs1659412

Variant names:

• chr9-84663237-G-A
• rs1659412

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 0.895 in 152,248 control chromosomes in the GnomAD database, including 61,048 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 0.89 (61048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.895 AC: 136104 AN: 152130 Hom.: 60996 Cov.: 32

Gnomad AFR AF: 0.859

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.896

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.895 AC: 136215 AN: 152248 Hom.: 61048 Cov.: 32 AF XY: 0.897 AC XY: 66781 AN XY: 74426

African (AFR) AF: 0.859 AC: 35671 AN: 41524

American (AMR) AF: 0.935 AC: 14299 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3112 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5175 AN: 5180

South Asian (SAS) AF: 0.964 AC: 4656 AN: 4828

European-Finnish (FIN) AF: 0.878 AC: 9304 AN: 10598

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.896 AC: 60945 AN: 68028

Other (OTH) AF: 0.920 AC: 1944 AN: 2112

Alfa AF: 0.896 Hom.: 53999

Bravo AF: 0.896

Asia WGS AF: 0.967 AC: 3357 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.53
DANN	Benign	0.52
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs1659412; hg19: chr9-87278152;