rs7723053

chr5-3347611-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 0.401 in 152,074 control chromosomes in the GnomAD database, including 12,626 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 0.40 (12626 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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: 0.401 AC: 60912 AN: 151958 Hom.: 12612 Cov.: 33

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.401 AC: 60964 AN: 152074 Hom.: 12626 Cov.: 33 AF XY: 0.405 AC XY: 30121 AN XY: 74346

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.384

Alfa AF: 0.398 Hom.: 2088

Bravo AF: 0.405

Asia WGS AF: 0.372 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.11
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7723053; hg19: chr5-3347725;