rs347245

Positions:

• chr5-73497226-A-G
• chr5-73497226-A-T

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 0.515 in 152,124 control chromosomes in the GnomAD database, including 22,535 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 0.52 (22535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.538

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.722 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: 0.516 AC: 78401 AN: 152006 Hom.: 22535 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.515 AC: 78415 AN: 152124 Hom.: 22535 Cov.: 32 AF XY: 0.518 AC XY: 38497 AN XY: 74358

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.470

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.542

Alfa AF: 0.621 Hom.: 59061

Bravo AF: 0.511

Asia WGS AF: 0.592 AC: 2060 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	9.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs347245; hg19: chr5-72793051;