rs2017620

Variant names:

• chr7-5796087-A-G
• rs2017620

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;