rs2017620

Positions:

• chr7-5796087-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 0.353 in 151,836 control chromosomes in the GnomAD database, including 10,903 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 0.35 (10903 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.5796087A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53649 AN: 151718 Hom.: 10904 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.353 AC: 53645 AN: 151836 Hom.: 10903 Cov.: 31 AF XY: 0.356 AC XY: 26410 AN XY: 74172

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.745

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.411

Gnomad4 OTH AF: 0.408

Alfa AF: 0.397 Hom.: 5803

Bravo AF: 0.342

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2017620; hg19: chr7-5835718;