chr1-143478759-A-T

Variant names:

• chr1-143478759-A-T
• rs226771

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614100.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KMT2CP3	ENST00000614100.1	TSL:6	n.146+671T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 6358 AN: 44500 Hom.: 668 Cov.: 5

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.187 AC: 2762 AN: 14766

American (AMR) AF: 0.100 AC: 555 AN: 5546

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 149 AN: 872

East Asian (EAS) AF: 0.0428 AC: 120 AN: 2804

South Asian (SAS) AF: 0.0802 AC: 126 AN: 1572

European-Finnish (FIN) AF: 0.156 AC: 318 AN: 2036

Middle Eastern (MID) AF: 0.129 AC: 9 AN: 70

European-Non Finnish (NFE) AF: 0.140 AC: 2246 AN: 16022

Other (OTH) AF: 0.0855 AC: 47 AN: 550

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.551 Hom.: 2488

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.47
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs226771; hg19: chr1-148874193;