17-10954761-A-G

Variant names:

• chr17-10954761-A-G
• rs852322

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 0.471 in 151,914 control chromosomes in the GnomAD database, including 19,137 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 0.47 (19137 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 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: 0.471 AC: 71440 AN: 151798 Hom.: 19090 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.471 AC: 71552 AN: 151914 Hom.: 19137 Cov.: 31 AF XY: 0.479 AC XY: 35572 AN XY: 74238

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.671

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.403

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.430

Alfa AF: 0.410 Hom.: 1716

Bravo AF: 0.488

Asia WGS AF: 0.609 AC: 2121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs852322; hg19: chr17-10858078;