chr22-19746288-G-A

Variant names:

• chr22-19746288-G-A
• rs7293017

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 0.138 in 152,074 control chromosomes in the GnomAD database, including 1,705 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 0.14 (1705 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.138 AC: 20988 AN: 151956 Hom.: 1711 Cov.: 33

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.138 AC: 20987 AN: 152074 Hom.: 1705 Cov.: 33 AF XY: 0.140 AC XY: 10402 AN XY: 74340

African (AFR) AF: 0.118 AC: 4897 AN: 41492

American (AMR) AF: 0.144 AC: 2201 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 837 AN: 3472

East Asian (EAS) AF: 0.395 AC: 2023 AN: 5128

South Asian (SAS) AF: 0.189 AC: 908 AN: 4816

European-Finnish (FIN) AF: 0.114 AC: 1204 AN: 10580

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8348 AN: 67972

Other (OTH) AF: 0.148 AC: 311 AN: 2104

Alfa AF: 0.132 Hom.: 1676

Bravo AF: 0.142

Asia WGS AF: 0.232 AC: 808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.56
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7293017; hg19: chr22-19733811;