2-85059326-G-C

Variant names:

• chr2-85059326-G-C
• rs2272512
• NM_020122.5:c.*5917G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020122.5(KCMF1):​c.*5917G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0795 in 152,184 control chromosomes in the GnomAD database, including 727 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 0.080 (727 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCMF1 NM_020122.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020122.5. 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
	KCMF1	NM_020122.5	MANE Select	c.*5917G>C		3_prime_UTR	Exon 7 of 7	NP_064507.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCMF1	ENST00000409785.9	TSL:1 MANE Select	c.*5917G>C		3_prime_UTR	Exon 7 of 7	ENSP00000386738.3	Q9P0J7
	LINC01964	ENST00000745932.1		n.368+1990C>G		intron	N/A
	LINC01964	ENST00000745933.1		n.314+1990C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0795 AC: 12091 AN: 152066 Hom.: 723 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0691

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.0510

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0693

Gnomad OTH AF: 0.0850

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0795 AC: 12104 AN: 152184 Hom.: 727 Cov.: 32 AF XY: 0.0824 AC XY: 6127 AN XY: 74390

African (AFR) AF: 0.0660 AC: 2743 AN: 41540

American (AMR) AF: 0.0691 AC: 1056 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0781 AC: 271 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1778 AN: 5174

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4822

European-Finnish (FIN) AF: 0.104 AC: 1099 AN: 10568

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0693 AC: 4710 AN: 68000

Other (OTH) AF: 0.0870 AC: 184 AN: 2116

Alfa AF: 0.0370 Hom.: 21

Bravo AF: 0.0785

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.097
DANN	Benign	0.49
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs2272512; hg19: chr2-85286449;