chr1-22689513-T-C

Variant names:

• chr1-22689513-T-C
• rs294223

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 0.744 in 151,890 control chromosomes in the GnomAD database, including 42,897 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 (42897 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 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: 0.744 AC: 112890 AN: 151772 Hom.: 42850 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.650

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.744 AC: 112996 AN: 151890 Hom.: 42897 Cov.: 31 AF XY: 0.735 AC XY: 54546 AN XY: 74206

African (AFR) AF: 0.896 AC: 37138 AN: 41434

American (AMR) AF: 0.657 AC: 10020 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.748 AC: 2596 AN: 3470

East Asian (EAS) AF: 0.454 AC: 2338 AN: 5146

South Asian (SAS) AF: 0.635 AC: 3049 AN: 4802

European-Finnish (FIN) AF: 0.650 AC: 6838 AN: 10526

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48455 AN: 67946

Other (OTH) AF: 0.757 AC: 1600 AN: 2114

Alfa AF: 0.711 Hom.: 19354

Bravo AF: 0.752

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.54
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs294223; hg19: chr1-23016006;