17-796780-T-C

Variant names:

• chr17-796780-T-C
• rs623323

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 0.791 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
• Publications: 34 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.589 AC: 24420 AN: 41442

American (AMR) AF: 0.859 AC: 13129 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.874 AC: 3034 AN: 3472

East Asian (EAS) AF: 0.891 AC: 4597 AN: 5160

South Asian (SAS) AF: 0.882 AC: 4251 AN: 4820

European-Finnish (FIN) AF: 0.852 AC: 9004 AN: 10574

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.868 AC: 59015 AN: 67990

Other (OTH) AF: 0.819 AC: 1725 AN: 2106

Alfa AF: 0.838 Hom.: 113979

Bravo AF: 0.784

Asia WGS AF: 0.843 AC: 2928 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.52
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs623323; hg19: chr17-700020;