7-22755802-C-G

Variant names:

• chr7-22755802-C-G
• rs1524103

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 0.305 in 151,628 control chromosomes in the GnomAD database, including 7,768 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 0.30 (7768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 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: 0.304 AC: 46089 AN: 151506 Hom.: 7740 Cov.: 31

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.305 AC: 46176 AN: 151628 Hom.: 7768 Cov.: 31 AF XY: 0.304 AC XY: 22508 AN XY: 74036

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.346

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.337

Alfa AF: 0.254 Hom.: 688

Bravo AF: 0.322

Asia WGS AF: 0.277 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524103; hg19: chr7-22795421;