chr5-60588490-C-T

Position:

• chr5-60588490-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 0.735 in 152,010 control chromosomes in the GnomAD database, including 42,226 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 0.73 (42226 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.60588490C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111549 AN: 151892 Hom.: 42162 Cov.: 32

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.735 AC: 111668 AN: 152010 Hom.: 42226 Cov.: 32 AF XY: 0.728 AC XY: 54093 AN XY: 74278

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.707

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.722

Alfa AF: 0.730 Hom.: 7761

Bravo AF: 0.748

Asia WGS AF: 0.658 AC: 2289 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2409791; hg19: chr5-59884317;