rs226771

Positions:

• chr1-143478759-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000614100.1(KMT2CP3):​n.146+671T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.14 (668 hom., cov: 5)
  • Failed GnomAD Quality Control
• Consequence: KMT2CP3 ENST00000614100.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

KMT2CP3 (HGNC:56181): (lysine methyltransferase 2C pseudogene 3)

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KMT2CP3	ENST00000614100.1	n.146+671T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6358 AN: 44500 Hom.: 668 Cov.: 5 FAILED QC

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.138

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.0858

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.143 AC: 6367 AN: 44554 Hom.: 668 Cov.: 5 AF XY: 0.144 AC XY: 3162 AN XY: 21998

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.0802

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.0855

Alfa AF: 0.551 Hom.: 2488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs226771; hg19: chr1-148874193;