rs4722172

Variant names:

• chr7-22746913-G-A
• rs4722172

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 0.868 in 152,210 control chromosomes in the GnomAD database, including 57,926 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 0.87 (57926 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.868 AC: 132064 AN: 152092 Hom.: 57859 Cov.: 32

Gnomad AFR AF: 0.962

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.953

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.884

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

GnomAD4 genome AF: 0.868 AC: 132191 AN: 152210 Hom.: 57926 Cov.: 32 AF XY: 0.874 AC XY: 65016 AN XY: 74400

African (AFR) AF: 0.962 AC: 39999 AN: 41558

American (AMR) AF: 0.903 AC: 13792 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3106 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5184 AN: 5188

South Asian (SAS) AF: 0.953 AC: 4598 AN: 4826

European-Finnish (FIN) AF: 0.831 AC: 8796 AN: 10584

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53808 AN: 67986

Other (OTH) AF: 0.885 AC: 1870 AN: 2112

Alfa AF: 0.863 Hom.: 17303

Bravo AF: 0.878

Asia WGS AF: 0.969 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.45
DANN	Benign	0.71
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs4722172; hg19: chr7-22786532;