rs10516446

Variant names:

• chr4-99629967-T-A
• rs10516446

Your query was ambiguous. Multiple possible variants found:

• chr4-99629967-T-A
• chr4-99629967-T-C
• chr4-99629967-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;