rs1423515

Positions:

• chr5-82766725-G-A

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 0.0571 in 152,044 control chromosomes in the GnomAD database, including 287 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 0.057 (287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 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: 0.0570 AC: 8662 AN: 151926 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0839

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.0375

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0385

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0500

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0571 AC: 8683 AN: 152044 Hom.: 287 Cov.: 32 AF XY: 0.0572 AC XY: 4256 AN XY: 74352

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.0313

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.0377

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0385

Gnomad4 NFE AF: 0.0500

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0555 Hom.: 154

Bravo AF: 0.0572

Asia WGS AF: 0.0990 AC: 347 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1423515; hg19: chr5-82062544; COSMIC: COSV72678553;