5-2706507-T-C

Position:

• chr5-2706507-T-C

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 0.586 in 151,810 control chromosomes in the GnomAD database, including 26,569 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 0.59 (26569 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.2706507T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.587 AC: 88986 AN: 151692 Hom.: 26578 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.649

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.586 AC: 88994 AN: 151810 Hom.: 26569 Cov.: 31 AF XY: 0.585 AC XY: 43392 AN XY: 74178

Gnomad4 AFR AF: 0.494

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.369

Gnomad4 SAS AF: 0.647

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.605

Alfa AF: 0.476 Hom.: 1616

Bravo AF: 0.578

Asia WGS AF: 0.501 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2962594; hg19: chr5-2706621;