17-796780-T-C

Variant names:

• chr17-796780-T-C
• rs623323

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 0.791 in 152,058 control chromosomes in the GnomAD database, including 48,769 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 0.79 (48769 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.869 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: 0.791 AC: 120201 AN: 151942 Hom.: 48775 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.869

Gnomad NFE AF: 0.868

Gnomad OTH AF: 0.821

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

GnomAD4 genome AF: 0.791 AC: 120225 AN: 152058 Hom.: 48769 Cov.: 31 AF XY: 0.793 AC XY: 58956 AN XY: 74328

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.859

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.891

Gnomad4 SAS AF: 0.882

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.868

Gnomad4 OTH AF: 0.819

Alfa AF: 0.861 Hom.: 76641

Bravo AF: 0.784

Asia WGS AF: 0.843 AC: 2928 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs623323; hg19: chr17-700020;