17-78637883-A-G

Variant names:

• chr17-78637883-A-G
• rs4796827

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 0.497 in 150,082 control chromosomes in the GnomAD database, including 20,011 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 0.50 (20011 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.626 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: 0.497 AC: 74593 AN: 149958 Hom.: 20018 Cov.: 25

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.497 AC: 74599 AN: 150082 Hom.: 20011 Cov.: 25 AF XY: 0.498 AC XY: 36467 AN XY: 73226

African (AFR) AF: 0.270 AC: 11011 AN: 40722

American (AMR) AF: 0.521 AC: 7803 AN: 14970

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2133 AN: 3454

East Asian (EAS) AF: 0.645 AC: 3238 AN: 5020

South Asian (SAS) AF: 0.593 AC: 2799 AN: 4722

European-Finnish (FIN) AF: 0.582 AC: 5967 AN: 10260

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 39916 AN: 67658

Other (OTH) AF: 0.526 AC: 1095 AN: 2080

Alfa AF: 0.553 Hom.: 49898

Bravo AF: 0.483

Asia WGS AF: 0.570 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.2
DANN	Benign	0.58
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs4796827; hg19: chr17-76633965;