chr5-74015515-A-G

Position:

• chr5-74015515-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 0.452 in 152,012 control chromosomes in the GnomAD database, including 18,931 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 0.45 (18931 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.74015515A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68542 AN: 151894 Hom.: 18876 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.452 AC: 68654 AN: 152012 Hom.: 18931 Cov.: 32 AF XY: 0.451 AC XY: 33505 AN XY: 74296

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.437

Alfa AF: 0.386 Hom.: 3544

Bravo AF: 0.485

Asia WGS AF: 0.439 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7700504; hg19: chr5-73311340;