rs7722413

chr5-138942562-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 0.352 in 152,054 control chromosomes in the GnomAD database, including 10,339 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 0.35 (10339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.519 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: 0.352 AC: 53523 AN: 151936 Hom.: 10318 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.352 AC: 53586 AN: 152054 Hom.: 10339 Cov.: 32 AF XY: 0.347 AC XY: 25822 AN XY: 74336

Gnomad4 AFR AF: 0.525

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.0491

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.295

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.312

Alfa AF: 0.307 Hom.: 9445

Bravo AF: 0.355

Asia WGS AF: 0.163 AC: 568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
Cadd	Benign	0.16
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7722413; hg19: chr5-138278251; COSMIC: COSV54529912;