rs10521141

Positions:

• chr16-27023153-T-C

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 0.553 in 152,142 control chromosomes in the GnomAD database, including 23,674 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 0.55 (23674 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

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 (NFE) allele frequency at 95% confidence interval = 0.583 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: 0.554 AC: 84161 AN: 152024 Hom.: 23664 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.553 AC: 84201 AN: 152142 Hom.: 23674 Cov.: 33 AF XY: 0.544 AC XY: 40456 AN XY: 74396

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.528

Alfa AF: 0.561 Hom.: 4519

Bravo AF: 0.553

Asia WGS AF: 0.377 AC: 1315 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	0.23
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521141; hg19: chr16-27034474;