rs1423515

Variant names:

• chr5-82766725-G-A
• rs1423515

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0841 AC: 3491 AN: 41486

American (AMR) AF: 0.0313 AC: 478 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0112 AC: 39 AN: 3468

East Asian (EAS) AF: 0.0377 AC: 195 AN: 5168

South Asian (SAS) AF: 0.112 AC: 538 AN: 4824

European-Finnish (FIN) AF: 0.0385 AC: 406 AN: 10544

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.0500 AC: 3401 AN: 67964

Other (OTH) AF: 0.0464 AC: 98 AN: 2112

Alfa AF: 0.0546 Hom.: 525

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
PhyloP100		1.2

Splicing

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

Other links and lift over

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