rs852321

chr17-10954126-T-Cchr17-10954126-T-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 0.449 in 152,058 control chromosomes in the GnomAD database, including 16,951 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 0.45 (16951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.652 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: 0.449 AC: 68230 AN: 151940 Hom.: 16915 Cov.: 32

Gnomad AFR AF: 0.636

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.449 AC: 68324 AN: 152058 Hom.: 16951 Cov.: 32 AF XY: 0.458 AC XY: 34035 AN XY: 74326

Gnomad4 AFR AF: 0.636

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.412

Alfa AF: 0.394 Hom.: 3004

Bravo AF: 0.464

Asia WGS AF: 0.594 AC: 2066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.0070
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852321; hg19: chr17-10857443;