rs2587613

chr18-41584521-G-A

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KC6	ENST00000595135.5	n.309+9825C>T		intron_variant, non_coding_transcript_variant		3
KC6	ENST00000593577.2	n.252+9825C>T		intron_variant, non_coding_transcript_variant		4
KC6	ENST00000599934.1	n.126-19623C>T		intron_variant, non_coding_transcript_variant		4
KC6	ENST00000600183.5	n.76+47479C>T		intron_variant, non_coding_transcript_variant		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;