5-83720924-C-T

Position:

• chr5-83720924-C-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 0.746 in 150,598 control chromosomes in the GnomAD database, including 41,778 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 0.75 (41746 hom., cov: 30)
  • Exomes 𝑓: 0.71 (32 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.83720924C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.746 AC: 112113 AN: 150366 Hom.: 41704 Cov.: 30

Gnomad AFR AF: 0.759

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.756

GnomAD4 exome AF: 0.710 AC: 88 AN: 124 Hom.: 32 Cov.: 0 AF XY: 0.744 AC XY: 67 AN XY: 90

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 1.00

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.400

Gnomad4 NFE exome AF: 0.729

Gnomad4 OTH exome AF: 0.833

GnomAD4 genome AF: 0.746 AC: 112208 AN: 150474 Hom.: 41746 Cov.: 30 AF XY: 0.738 AC XY: 54259 AN XY: 73514

Gnomad4 AFR AF: 0.760

Gnomad4 AMR AF: 0.739

Gnomad4 ASJ AF: 0.728

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.760

Alfa AF: 0.753 Hom.: 3877

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3734092; hg19: chr5-83016743;