rs4722172

Positions:

• chr7-22746913-G-A

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 0.868 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.962

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.953

Gnomad4 FIN AF: 0.831

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.885

Alfa AF: 0.821 Hom.: 10682

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4722172; hg19: chr7-22786532;