rs852321

Variant names:

• chr17-10954126-T-C
• rs852321

Your query was ambiguous. Multiple possible variants found:

• chr17-10954126-T-C
• chr17-10954126-T-G

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 0.449 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.636 AC: 26366 AN: 41462

American (AMR) AF: 0.468 AC: 7142 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 895 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3467 AN: 5172

South Asian (SAS) AF: 0.498 AC: 2400 AN: 4824

European-Finnish (FIN) AF: 0.402 AC: 4251 AN: 10574

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.330 AC: 22457 AN: 67978

Other (OTH) AF: 0.412 AC: 870 AN: 2114

Alfa AF: 0.459 Hom.: 8429

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
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs852321; hg19: chr17-10857443;