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. The variant received -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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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

African (AFR) AF: 0.730 AC: 30268 AN: 41436

American (AMR) AF: 0.569 AC: 8672 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1991 AN: 3472

East Asian (EAS) AF: 0.136 AC: 698 AN: 5150

South Asian (SAS) AF: 0.579 AC: 2797 AN: 4828

European-Finnish (FIN) AF: 0.593 AC: 6250 AN: 10538

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.578 AC: 39282 AN: 67952

Other (OTH) AF: 0.558 AC: 1176 AN: 2106

Alfa AF: 0.576 Hom.: 108819

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
PhyloP100		-0.021

Splicing

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

Other links and lift over

dbSNP: rs994390; hg19: chr9-26538805;