rs10516451

Variant names:

• chr4-99705392-A-G
• rs10516451

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 0.671 in 152,000 control chromosomes in the GnomAD database, including 35,288 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 0.67 (35288 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 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: 0.671 AC: 101852 AN: 151882 Hom.: 35244 Cov.: 31

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.769

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.671 AC: 101953 AN: 152000 Hom.: 35288 Cov.: 31 AF XY: 0.668 AC XY: 49585 AN XY: 74268

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.593

Gnomad4 ASJ AF: 0.769

Gnomad4 EAS AF: 0.766

Gnomad4 SAS AF: 0.659

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.664

Alfa AF: 0.618 Hom.: 39569

Bravo AF: 0.680

Asia WGS AF: 0.662 AC: 2295 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.15
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516451; hg19: chr4-100626549;