rs2587613

Variant names:

• chr18-41584521-G-A
• rs2587613
• ENST00000593577.2:n.252+9825C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000595135.5(KC6):​n.309+9825C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,026 control chromosomes in the GnomAD database, including 4,368 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 0.21 (4368 hom., cov: 32)
• Consequence: KC6 ENST00000595135.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

KC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 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
KC6	ENST00000593577.2	n.252+9825C>T		intron_variant	Intron 2 of 4	4
KC6	ENST00000595135.5	n.309+9825C>T		intron_variant	Intron 2 of 4	3
KC6	ENST00000599934.1	n.126-19623C>T		intron_variant	Intron 1 of 3	4
KC6	ENST00000600183.5	n.76+47479C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32505 AN: 151906 Hom.: 4366 Cov.: 32

Gnomad AFR AF: 0.0541

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.214 AC: 32505 AN: 152026 Hom.: 4368 Cov.: 32 AF XY: 0.216 AC XY: 16057 AN XY: 74312

Gnomad4 AFR AF: 0.0539

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.0923

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.217

Alfa AF: 0.258 Hom.: 2843

Bravo AF: 0.192

Asia WGS AF: 0.105 AC: 367 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2587613; hg19: chr18-39164485;