rs10521243

chr16-51667187-G-Achr16-51667187-G-T

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 0.076 in 151,982 control chromosomes in the GnomAD database, including 1,283 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 0.076 (1283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138

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 (AFR) allele frequency at 95% confidence interval = 0.242 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: 0.0758 AC: 11517 AN: 151864 Hom.: 1281 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0268

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.0483

Gnomad SAS AF: 0.0426

Gnomad FIN AF: 0.0000951

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00407

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0760 AC: 11546 AN: 151982 Hom.: 1283 Cov.: 32 AF XY: 0.0740 AC XY: 5493 AN XY: 74254

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.0267

Gnomad4 ASJ AF: 0.0205

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.0422

Gnomad4 FIN AF: 0.0000951

Gnomad4 NFE AF: 0.00407

Gnomad4 OTH AF: 0.0560

Alfa AF: 0.0162 Hom.: 60

Bravo AF: 0.0840

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	8.4
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521243; hg19: chr16-51701098;