18-41477761-G-C

Variant names:

• chr18-41477761-G-C
• rs2848745
• ENST00000600644.2:n.313+2995C>G

Variant summary

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

The ENST00000600644.2(KC6):​n.313+2995C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,968 control chromosomes in the GnomAD database, including 15,496 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 0.41 (15496 hom., cov: 32)
• Consequence: KC6 ENST00000600644.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

KC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.586 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	ENST00000600644.2	n.313+2995C>G		intron_variant	Intron 1 of 1	3
ENSG00000286328	ENST00000670702.1	n.200-26373G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62418 AN: 151850 Hom.: 15484 Cov.: 32

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.411 AC: 62436 AN: 151968 Hom.: 15496 Cov.: 32 AF XY: 0.413 AC XY: 30667 AN XY: 74244

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.603

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.444

Alfa AF: 0.367 Hom.: 1401

Bravo AF: 0.385

Asia WGS AF: 0.509 AC: 1764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2848745; hg19: chr18-39057725;