17-10954761-A-G

Variant names:

• chr17-10954761-A-G
• rs852322

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 0.471 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.710 AC: 29419 AN: 41418

American (AMR) AF: 0.477 AC: 7278 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3468

East Asian (EAS) AF: 0.671 AC: 3455 AN: 5150

South Asian (SAS) AF: 0.497 AC: 2391 AN: 4814

European-Finnish (FIN) AF: 0.403 AC: 4243 AN: 10522

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22486 AN: 67958

Other (OTH) AF: 0.430 AC: 908 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.46
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs852322; hg19: chr17-10858078;