rs10516451

Positions:

• chr4-99705392-A-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 0.671 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;