chr22-17733496-G-C

Variant names:

• chr22-17733496-G-C
• rs3747026

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 0.454 in 152,084 control chromosomes in the GnomAD database, including 16,485 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 0.45 (16485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.786 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: 0.454 AC: 68965 AN: 151966 Hom.: 16486 Cov.: 33

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.583

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.454 AC: 68999 AN: 152084 Hom.: 16485 Cov.: 33 AF XY: 0.462 AC XY: 34369 AN XY: 74340

African (AFR) AF: 0.359 AC: 14900 AN: 41480

American (AMR) AF: 0.563 AC: 8608 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1551 AN: 3470

East Asian (EAS) AF: 0.807 AC: 4172 AN: 5172

South Asian (SAS) AF: 0.602 AC: 2898 AN: 4816

European-Finnish (FIN) AF: 0.463 AC: 4892 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30347 AN: 67978

Other (OTH) AF: 0.463 AC: 979 AN: 2114

Alfa AF: 0.271 Hom.: 644

Bravo AF: 0.460

Asia WGS AF: 0.666 AC: 2314 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	0.35
DANN	Benign	0.44
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3747026; hg19: chr22-18216262;