chr7-52725576-C-A

Variant names:

• chr7-52725576-C-A
• rs1230545

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B.

Score: -12 - Benign

-12

BP4_StrongBA1

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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.241 AC: 10006 AN: 41434

American (AMR) AF: 0.199 AC: 3043 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.275 AC: 953 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1020 AN: 5156

South Asian (SAS) AF: 0.205 AC: 990 AN: 4826

European-Finnish (FIN) AF: 0.225 AC: 2383 AN: 10576

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.196 AC: 13315 AN: 67986

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.204 Hom.: 12656

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
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1230545; hg19: chr7-52793270;