chr5-2202071-A-G

Position:

• chr5-2202071-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 0.646 in 152,162 control chromosomes in the GnomAD database, including 32,015 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 0.65 (32015 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2202071A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98249 AN: 152042 Hom.: 31979 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.653

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

GnomAD4 genome AF: 0.646 AC: 98335 AN: 152162 Hom.: 32015 Cov.: 33 AF XY: 0.643 AC XY: 47799 AN XY: 74374

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.649

Alfa AF: 0.627 Hom.: 17014

Bravo AF: 0.656

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2897241; hg19: chr5-2202185;