rs10516446

chr4-99629967-T-Achr4-99629967-T-Cchr4-99629967-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 0.197 in 152,114 control chromosomes in the GnomAD database, including 3,315 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 0.20 (3315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

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 (EAS) allele frequency at 95% confidence interval = 0.427 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: 0.197 AC: 29958 AN: 151996 Hom.: 3314 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.0944

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.197 AC: 29970 AN: 152114 Hom.: 3315 Cov.: 32 AF XY: 0.196 AC XY: 14603 AN XY: 74366

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.442

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.0944

Gnomad4 NFE AF: 0.179

Gnomad4 OTH AF: 0.208

Alfa AF: 0.184 Hom.: 319

Bravo AF: 0.202

Asia WGS AF: 0.290 AC: 1010 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.6
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516446; hg19: chr4-100551124;