chr5-60588490-C-T

Variant names:

• chr5-60588490-C-T
• rs2409791

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;