rs1364043

chr5-63955024-T-G

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 0.248 in 152,040 control chromosomes in the GnomAD database, including 5,130 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 0.25 (5130 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 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: 0.248 AC: 37650 AN: 151920 Hom.: 5119 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.248 AC: 37662 AN: 152040 Hom.: 5130 Cov.: 32 AF XY: 0.252 AC XY: 18717 AN XY: 74298

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.249

Alfa AF: 0.243 Hom.: 9747

Bravo AF: 0.245

Asia WGS AF: 0.481 AC: 1672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.010
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1364043; hg19: chr5-63250851;