2-85059396-T-C

Variant names:

• chr2-85059396-T-C
• rs2272514
• NM_020122.5:c.*5987T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_020122.5(KCMF1):​c.*5987T>C 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: 32)
• Consequence: KCMF1 NM_020122.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.194
• Publications: 3 publications found

Genes affected

KCMF1 (HGNC:20589): (potassium channel modulatory factor 1) Enables ubiquitin protein ligase activity. Predicted to be involved in synaptic signaling. Located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

LINC01964 (HGNC:52789): (long intergenic non-protein coding RNA 1964)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCMF1	NM_020122.5	c.*5987T>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000409785.9	NP_064507.3
KCMF1	XM_006712052.4	c.*5987T>C		3_prime_UTR_variant	Exon 7 of 7		XP_006712115.1
KCMF1	XM_047445126.1	c.*5987T>C		3_prime_UTR_variant	Exon 8 of 8		XP_047301082.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCMF1	ENST00000409785.9	c.*5987T>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_020122.5	ENSP00000386738.3
LINC01964	ENST00000745932.1	n.368+1920A>G		intron_variant	Intron 2 of 6
LINC01964	ENST00000745933.1	n.314+1920A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 1145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.53
PhyloP100		0.19

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: rs2272514; hg19: chr2-85286519;