chr17-10958389-A-G

Variant names:

• chr17-10958389-A-G
• rs2321313

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 151,948 control chromosomes in the GnomAD database, including 18,471 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 (18471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.405
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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: 71448 AN: 151830 Hom.: 18440 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.471 AC: 71538 AN: 151948 Hom.: 18471 Cov.: 32 AF XY: 0.476 AC XY: 35306 AN XY: 74234

African (AFR) AF: 0.679 AC: 28144 AN: 41440

American (AMR) AF: 0.482 AC: 7361 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 901 AN: 3462

East Asian (EAS) AF: 0.603 AC: 3119 AN: 5172

South Asian (SAS) AF: 0.472 AC: 2272 AN: 4814

European-Finnish (FIN) AF: 0.396 AC: 4171 AN: 10530

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24233 AN: 67948

Other (OTH) AF: 0.422 AC: 890 AN: 2108

Alfa AF: 0.431 Hom.: 1926

Bravo AF: 0.487

Asia WGS AF: 0.567 AC: 1975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.73
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2321313; hg19: chr17-10861706;