rs2026406

Variant names:

• chr9-75455766-G-C
• rs2026406

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 0.498 in 152,084 control chromosomes in the GnomAD database, including 19,437 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 0.50 (19437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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: 0.498 AC: 75658 AN: 151966 Hom.: 19426 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.498 AC: 75705 AN: 152084 Hom.: 19437 Cov.: 33 AF XY: 0.499 AC XY: 37119 AN XY: 74324

Gnomad4 AFR AF: 0.429 AC: 0.428747 AN: 0.428747

Gnomad4 AMR AF: 0.553 AC: 0.55258 AN: 0.55258

Gnomad4 ASJ AF: 0.434 AC: 0.433756 AN: 0.433756

Gnomad4 EAS AF: 0.312 AC: 0.312136 AN: 0.312136

Gnomad4 SAS AF: 0.312 AC: 0.312422 AN: 0.312422

Gnomad4 FIN AF: 0.657 AC: 0.656694 AN: 0.656694

Gnomad4 NFE AF: 0.535 AC: 0.534754 AN: 0.534754

Gnomad4 OTH AF: 0.502 AC: 0.502367 AN: 0.502367

Alfa AF: 0.522 Hom.: 2612

Bravo AF: 0.490

Asia WGS AF: 0.287 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2026406; hg19: chr9-78070682;