rs2272513

chr2-85059359-T-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCMF1	NM_020122.5	c.*5950T>A		3_prime_UTR_variant	7/7	ENST00000409785.9
KCMF1	XM_006712052.4	c.*5950T>A		3_prime_UTR_variant	7/7
KCMF1	XM_047445126.1	c.*5950T>A		3_prime_UTR_variant	8/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCMF1	ENST00000409785.9	c.*5950T>A		3_prime_UTR_variant	7/7	1	NM_020122.5	P1

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

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

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.347

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0885

Gnomad4 OTH AF: 0.125

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.34
Dann	Benign	0.39

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

Publications

LitVar

Other links and lift over

dbSNP: rs2272513; hg19: chr2-85286482;