rs852320

Variant names:

• chr17-10953769-T-G
• rs852320

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 0.309 in 152,216 control chromosomes in the GnomAD database, including 8,358 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 0.31 (8358 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.476 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: 0.308 AC: 46919 AN: 152098 Hom.: 8342 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.309 AC: 46974 AN: 152216 Hom.: 8358 Cov.: 33 AF XY: 0.312 AC XY: 23210 AN XY: 74444

African (AFR) AF: 0.481 AC: 19974 AN: 41500

American (AMR) AF: 0.351 AC: 5362 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3470

East Asian (EAS) AF: 0.169 AC: 877 AN: 5188

South Asian (SAS) AF: 0.379 AC: 1828 AN: 4824

European-Finnish (FIN) AF: 0.204 AC: 2167 AN: 10616

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15262 AN: 68002

Other (OTH) AF: 0.286 AC: 604 AN: 2114

Alfa AF: 0.255 Hom.: 3205

Bravo AF: 0.325

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.70
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs852320; hg19: chr17-10857086;