19-55348071-C-G

Variant names:

• chr19-55348071-C-G
• rs1058511
• NM_032701.4:c.*622C>G

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_032701.4(KMT5C):​c.*622C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
• Consequence: KMT5C NM_032701.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 20 publications found

Genes affected

KMT5C (HGNC:28405): (lysine methyltransferase 5C) SUV420H2 and the related enzyme SUV420H1 (MIM 610881) function as histone methyltransferases that specifically trimethylate nucleosomal histone H4 (see MIM 602822) on lysine-20 (K20) (Schotta et al., 2004 [PubMed 15145825]).[supplied by OMIM, Dec 2009]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_032701.4. 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
	KMT5C	NM_032701.4	MANE Select	c.*622C>G		3_prime_UTR	Exon 9 of 9	NP_116090.2
	KMT5C	NM_001438948.1		c.*622C>G		3_prime_UTR	Exon 9 of 9	NP_001425877.1
	KMT5C	NM_001438949.1		c.*622C>G		3_prime_UTR	Exon 8 of 8	NP_001425878.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KMT5C	ENST00000255613.8	TSL:1 MANE Select	c.*622C>G		3_prime_UTR	Exon 9 of 9	ENSP00000255613.3	Q86Y97-1
	KMT5C	ENST00000630497.1	TSL:1	c.*622C>G		3_prime_UTR	Exon 7 of 7	ENSP00000486397.1	A0A0D9SF94
	KMT5C	ENST00000943506.1		c.*622C>G		3_prime_UTR	Exon 9 of 9	ENSP00000613565.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	8.0
DANN	Benign	0.89
PhyloP100		0.20

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1058511; hg19: chr19-55859439;