chr17-78637883-A-G

Position:

• chr17-78637883-A-G

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 0.497 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.78637883A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.521

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.645

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.590

Gnomad4 OTH AF: 0.526

Alfa AF: 0.559 Hom.: 13066

Bravo AF: 0.483

Asia WGS AF: 0.570 AC: 1979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4796827; hg19: chr17-76633965;