rs10521277

chr17-14619634-G-A

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 0.235 in 152,008 control chromosomes in the GnomAD database, including 4,232 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 0.24 (4232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 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: 0.236 AC: 35771 AN: 151890 Hom.: 4227 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.251

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.235 AC: 35789 AN: 152008 Hom.: 4232 Cov.: 32 AF XY: 0.237 AC XY: 17604 AN XY: 74284

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.313

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.241

Alfa AF: 0.238 Hom.: 2382

Bravo AF: 0.237

Asia WGS AF: 0.301 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.1
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521277; hg19: chr17-14522951;