rs1230545

chr7-52725576-C-Achr7-52725576-C-G

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 0.213 in 152,034 control chromosomes in the GnomAD database, including 3,499 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 0.21 (3499 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32379 AN: 151916 Hom.: 3499 Cov.: 33

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.213 AC: 32399 AN: 152034 Hom.: 3499 Cov.: 33 AF XY: 0.213 AC XY: 15854 AN XY: 74326

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.196

Gnomad4 OTH AF: 0.220

Alfa AF: 0.203 Hom.: 5323

Bravo AF: 0.214

Asia WGS AF: 0.211 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.75
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1230545; hg19: chr7-52793270;