5-60588490-C-T

Variant names:

• chr5-60588490-C-T
• rs2409791

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.932 AC: 38726 AN: 41534

American (AMR) AF: 0.697 AC: 10621 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2455 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3274 AN: 5162

South Asian (SAS) AF: 0.556 AC: 2681 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6680 AN: 10556

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44918 AN: 67920

Other (OTH) AF: 0.722 AC: 1520 AN: 2106

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
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs2409791; hg19: chr5-59884317;