rs2326909

Variant names:

• chr20-7278822-A-G
• rs2326909

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 0.492 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
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.376 AC: 15570 AN: 41398

American (AMR) AF: 0.612 AC: 9332 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3466

East Asian (EAS) AF: 0.428 AC: 2194 AN: 5124

South Asian (SAS) AF: 0.523 AC: 2523 AN: 4820

European-Finnish (FIN) AF: 0.468 AC: 4920 AN: 10520

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

European-Non Finnish (NFE) AF: 0.537 AC: 36463 AN: 67886

Other (OTH) AF: 0.533 AC: 1125 AN: 2112

Alfa AF: 0.513 Hom.: 6881

Bravo AF: 0.497

Asia WGS AF: 0.508 AC: 1760 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.55
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2326909; hg19: chr20-7259469;