5-2403971-A-G

Variant names:

• chr5-2403971-A-G
• rs10052956

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 0.286 in 152,050 control chromosomes in the GnomAD database, including 6,392 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 0.29 (6392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 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: 0.286 AC: 43442 AN: 151932 Hom.: 6385 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.286 AC: 43472 AN: 152050 Hom.: 6392 Cov.: 32 AF XY: 0.288 AC XY: 21389 AN XY: 74316

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.246

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.260

Alfa AF: 0.260 Hom.: 2544

Bravo AF: 0.279

Asia WGS AF: 0.293 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.64
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10052956; hg19: chr5-2404085;