rs2962009

Positions:

• chr5-58179197-A-C
• chr5-58179197-A-G
• chr5-58179197-A-T

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 0.922 in 152,202 control chromosomes in the GnomAD database, including 64,833 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 0.92 (64833 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.943 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.58179197A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.922 AC: 140289 AN: 152084 Hom.: 64800 Cov.: 32

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.964

Gnomad AMR AF: 0.956

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.910

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.914

Gnomad OTH AF: 0.924

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

GnomAD4 genome AF: 0.922 AC: 140375 AN: 152202 Hom.: 64833 Cov.: 32 AF XY: 0.920 AC XY: 68424 AN XY: 74396

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.956

Gnomad4 ASJ AF: 0.914

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.914

Gnomad4 OTH AF: 0.921

Alfa AF: 0.918 Hom.: 31075

Bravo AF: 0.932

Asia WGS AF: 0.902 AC: 3139 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	0.23
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2962009; hg19: chr5-57475024;