5-7328063-G-C

Variant names:

• chr5-7328063-G-C
• rs2202445

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 0.304 in 152,106 control chromosomes in the GnomAD database, including 7,169 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 (7169 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 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: 46211 AN: 151990 Hom.: 7160 Cov.: 33

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.304 AC: 46244 AN: 152106 Hom.: 7169 Cov.: 33 AF XY: 0.305 AC XY: 22644 AN XY: 74364

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.393

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.322

Alfa AF: 0.0980 Hom.: 137

Bravo AF: 0.316

Asia WGS AF: 0.376 AC: 1307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2202445; hg19: chr5-7328176;