rs807669

Variant names:

• chr22-19167009-T-C
• rs807669

Your query was ambiguous. Multiple possible variants found:

• chr22-19167009-T-C
• chr22-19167009-T-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 0.737 in 152,130 control chromosomes in the GnomAD database, including 42,508 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 0.74 (42508 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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: 0.737 AC: 111967 AN: 152014 Hom.: 42440 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.737 AC: 112093 AN: 152130 Hom.: 42508 Cov.: 32 AF XY: 0.742 AC XY: 55184 AN XY: 74356

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.740

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.713

Alfa AF: 0.650 Hom.: 31767

Bravo AF: 0.745

Asia WGS AF: 0.892 AC: 3102 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.044
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs807669; hg19: chr22-19154522;