chr7-52654736-T-C

Position:

• chr7-52654736-T-C

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 152,074 control chromosomes in the GnomAD database, including 7,550 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 (7550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 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: 0.305 AC: 46334 AN: 151956 Hom.: 7546 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.305 AC: 46331 AN: 152074 Hom.: 7550 Cov.: 32 AF XY: 0.308 AC XY: 22871 AN XY: 74318

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.295

Alfa AF: 0.331 Hom.: 15829

Bravo AF: 0.288

Asia WGS AF: 0.195 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.22
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7810220; hg19: chr7-52722432;