rs2326909

Variant names:

• chr20-7278822-A-G
• rs2326909

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 0.492 in 151,778 control chromosomes in the GnomAD database, including 19,032 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 0.49 (19032 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

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 (AMR) allele frequency at 95% confidence interval = 0.602 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: 0.492 AC: 74643 AN: 151658 Hom.: 18996 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.492 AC: 74725 AN: 151778 Hom.: 19032 Cov.: 31 AF XY: 0.495 AC XY: 36687 AN XY: 74148

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.523

Gnomad4 FIN AF: 0.468

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.533

Alfa AF: 0.520 Hom.: 3508

Bravo AF: 0.497

Asia WGS AF: 0.508 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2326909; hg19: chr20-7259469;