rs994390

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;