rs9955346

Variant names:

• chr18-41546977-A-G
• rs9955346
• ENST00000593577.2:n.253-25481T>C

Your query was ambiguous. Multiple possible variants found:

• chr18-41546977-A-G
• chr18-41546977-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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KC6	ENST00000593577.2	n.253-25481T>C		intron_variant	Intron 2 of 4	4
KC6	ENST00000595135.5	n.310-30422T>C		intron_variant	Intron 2 of 4	3
KC6	ENST00000599934.1	n.225+17822T>C		intron_variant	Intron 2 of 3	4
KC6	ENST00000600183.5	n.77-21451T>C		intron_variant	Intron 1 of 2	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;