chr4-115863802-G-A

Variant names:

• chr4-115863802-G-A
• rs10516624

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 0.245 in 151,162 control chromosomes in the GnomAD database, including 4,802 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 (4802 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.245 AC: 37059 AN: 151040 Hom.: 4797 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.245 AC: 37089 AN: 151162 Hom.: 4802 Cov.: 31 AF XY: 0.243 AC XY: 17958 AN XY: 73866

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.261

Alfa AF: 0.259 Hom.: 659

Bravo AF: 0.243

Asia WGS AF: 0.241 AC: 838 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516624; hg19: chr4-116784958;