rs994390

Variant names:

• chr9-26538807-A-C
• rs994390

Your query was ambiguous. Multiple possible variants found:

• chr9-26538807-A-C
• chr9-26538807-A-G

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 0.605 in 151,934 control chromosomes in the GnomAD database, including 28,691 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 0.61 (28691 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0210

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 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: 0.605 AC: 91860 AN: 151816 Hom.: 28650 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.605 AC: 91959 AN: 151934 Hom.: 28691 Cov.: 31 AF XY: 0.602 AC XY: 44658 AN XY: 74244

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.578

Gnomad4 OTH AF: 0.558

Alfa AF: 0.567 Hom.: 49066

Bravo AF: 0.603

Asia WGS AF: 0.416 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs994390; hg19: chr9-26538805;