rs10521141

Variant names:

• chr16-27023153-T-C
• rs10521141

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.564 AC: 23406 AN: 41476

American (AMR) AF: 0.512 AC: 7833 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1560 AN: 5176

South Asian (SAS) AF: 0.426 AC: 2050 AN: 4816

European-Finnish (FIN) AF: 0.523 AC: 5542 AN: 10592

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39977 AN: 67996

Other (OTH) AF: 0.528 AC: 1115 AN: 2112

Alfa AF: 0.561 Hom.: 4642

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10521141; hg19: chr16-27034474;