rs1687390

Variant names:

• chr9-114327608-G-A
• rs1687390

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.126 in 149,142 control chromosomes in the GnomAD database, including 86 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 0.13 (86 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.900
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS2: High Homozygotes in GnomAd4 at 86 gene

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: 0.125 AC: 18700 AN: 149026 Hom.: 86 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0917

Gnomad AMR AF: 0.0917

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.00253

Gnomad SAS AF: 0.0219

Gnomad FIN AF: 0.0199

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0690

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.126 AC: 18726 AN: 149142 Hom.: 86 Cov.: 30 AF XY: 0.122 AC XY: 8878 AN XY: 72930

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.297 AC: 11839 AN: 39884

American (AMR) AF: 0.0914 AC: 1378 AN: 15074

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 197 AN: 3432

East Asian (EAS) AF: 0.00253 AC: 13 AN: 5134

South Asian (SAS) AF: 0.0209 AC: 100 AN: 4788

European-Finnish (FIN) AF: 0.0199 AC: 210 AN: 10546

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0691 AC: 4629 AN: 67038

Other (OTH) AF: 0.122 AC: 252 AN: 2060

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.110 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs1687390; hg19: chr9-117089888;