rs9955346

chr18-41546977-A-Gchr18-41546977-A-T

Variant summary

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

The ENST00000595135.5(KC6):n.310-30422T>C 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 0.154 in 152,176 control chromosomes in the GnomAD database, including 1,794 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 0.15 (1794 hom., cov: 32)
• Consequence: KC6 ENST00000595135.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

Genes affected

KC6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 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.310-30422T>C		intron_variant, non_coding_transcript_variant		3
KC6	ENST00000593577.2	n.253-25481T>C		intron_variant, non_coding_transcript_variant		4
KC6	ENST00000599934.1	n.225+17822T>C		intron_variant, non_coding_transcript_variant		4
KC6	ENST00000600183.5	n.77-21451T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23359 AN: 152058 Hom.: 1793 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.154 AC: 23373 AN: 152176 Hom.: 1794 Cov.: 32 AF XY: 0.153 AC XY: 11355 AN XY: 74402

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.162

Alfa AF: 0.156 Hom.: 1908

Bravo AF: 0.156

Asia WGS AF: 0.161 AC: 563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.5
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9955346; hg19: chr18-39126941;