rs2272513

Variant names:

• chr2-85059359-T-A
• rs2272513
• NM_020122.5:c.*5950T>A

Variant summary

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

The NM_020122.5(KCMF1):​c.*5950T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 152,194 control chromosomes in the GnomAD database, including 1,903 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 0.14 (1903 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: KCMF1 NM_020122.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.334 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCMF1	NM_020122.5	MANE Select	c.*5950T>A		3_prime_UTR	Exon 7 of 7	NP_064507.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KCMF1	ENST00000409785.9	TSL:1 MANE Select	c.*5950T>A		3_prime_UTR	Exon 7 of 7	ENSP00000386738.3
	LINC01964	ENST00000745932.1		n.368+1957A>T		intron	N/A
	LINC01964	ENST00000745933.1		n.314+1957A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20899 AN: 152076 Hom.: 1889 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.347

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0885

Gnomad OTH AF: 0.123

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

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.138 AC: 20949 AN: 152194 Hom.: 1903 Cov.: 32 AF XY: 0.140 AC XY: 10418 AN XY: 74410

African (AFR) AF: 0.217 AC: 9026 AN: 41510

American (AMR) AF: 0.0929 AC: 1420 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.347 AC: 1798 AN: 5182

South Asian (SAS) AF: 0.117 AC: 565 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1517 AN: 10578

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0885 AC: 6019 AN: 68024

Other (OTH) AF: 0.125 AC: 264 AN: 2114

Alfa AF: 0.114 Hom.: 154

Bravo AF: 0.137

Asia WGS AF: 0.200 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.34
DANN	Benign	0.39
PhyloP100		-0.87
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: rs2272513; hg19: chr2-85286482;